The following information was gleaned from the Info-LabVIEW mailing list, experimentation, and from emails from other wireworkers. If you know any others, or find any errors here, please enlighten me. Also check out the unknown settings.

The ones that I think are really useful are colored like this.

Most of these settings have been confirmed to work on LabVIEW 5.1.1 running under Windows 2000. A few unconfirmed settings are noted. If someone can confirm the functionality of these on any platform, or disprove the functionality on other platforms, please let me know.

There are also a few other undocumented settings that I logically grouped with the Colors, VI Server and Web Server settings.

Setting Description Type Default
checkActiveXLibs Unconfirmed. Set to True to enable more detailed checking of the ActiveX interface when LabVIEW starts up. An error message will appear if LabVIEW encounters an error. TF False
copyDeleteFPDCOFromFPTerm Setting this value True enables you to delete controls and indicators directly from the diagram by deleting the terminal.

In LV6 and above, this option is "Delete front panel terminals from diagram" in the Block Diagram section of the Options dialog.

TF False
ctlEditNoQuestions Setting this value True prevents the "Replace the original control…" dialog from appearing and ALWAYS does the replacement. TF False
debugging If set to True, LabVIEW reports all kinds of runtime checks to the file <lvdir>\dprintf.txt in the LabVIEW directory and if a debugger application is attached to LabVIEW it is also reported to that debuggers output stream or if no debugger is attached it is reported to the System debugger (Dr. Watson). TF False
defaultCtrlPalPos Specifies where the Controls palette will be placed when LV starts up. rect  
defaultFuncPalPos Specifies where the Functions palette will be placed when LV starts up. rect  
defPrecision Default precision for controls and indicators {Extended, Double, Single} string Double
dialogEditor Set to True to add "Load Dialog Script..." and "Save Dialog Script..." to the File menu. You can use these functions to modify LV's built-in dialogs. TF False
dithering Unconfirmed. PC and Mac. Specifies if dithering should be used when displaying higher color items on low color devices. TF  
editRTMenusFromRsrc Set this to True to add "Open From Rsrc..." and "Save To Rsrc..." to the File menu of the Menu Editor. You can then open LV's built-in menus in the *.rsc files. The warnings for the Dialog Editor also apply here. TF False
EnableAutoScales You can change the range of a graph's axis scale during run-time. In LabVIEW 6.0 and above, if the number of digits required to show the values increases, the plot area size is reduced to show the entire scale label. To prevent this automatic resizing of your plots, set this value to False.

For more information, read this article and this article in the NI KnowledgeBase.

TF True
enableGroupLock This setting enables the grouping and locking of front panel objects. These menu items will appear on the standard Reorder menu (where Move to Front/Back is located).
Grouped objects maintain their relative arrangement and can be moved together, while locked objects maintain their location on the front panel, and can not be deleted.
I found that this causes LV 5.1 to crash on occasion, but this has become a working, standard feature in LV 6.
TF LV5:False
enableMultiScales This setting enables multiple scales on waveform and XY graphs. Using multiple scales on a graph allows you to display multiple plots that do not share a common x- or y-scale.
I found that this is buggy in LV 5.1, but has become a working, standard feature in LV 6.
TF LV5:False
ESys.StdNParallel This setting defines the number of threads to start in each execution system and priority level.
0 is equivalent to turning off the Preferences menu item "Run with multiple threads".
1 is the default value, equivalent to turning on "Run with multiple threads".
2 to 8 defines a higher number of threads to start (i.e. a 5x5 matrix).
-1 tells LabVIEW to start with a custom set of threading parameters as defined by keys.
See description above. These settings are only enabled when set to -1.

xxx is a subsystem abbreviation (such as other1)

yyy is a priority (such as Normal or Vhigh)

These are the number of threads to create for the thread pools. LabVIEW does not change the priority of threads at run time.

LabVIEW 5.0 does not create any new threads after startup (except for some Win32 dialog boxes which create their own threads).

LabVIEW 5.1 will create threads for a subsystem if it loads a VI that is assigned to that subsystem.

Each subsystem has several "buckets" of threads for relative priorities. Each of these INI entries tells LabVIEW how many threads to start for the buckets.

forceBW Set this value True to tell the Icon Editor to create a default black&white icon if you don't create one. TF False
formulaBoxPrecision Precision for formula boxes {Extended, Double, Single}
Be careful. This is not only the default precision for new formula boxes, but this value will change the precision of existing formula boxes.
string Double
hideRootWindow Set this value to True to hide the "LabVIEW" taskbar button. This extra tab represents the initial LabVIEW window that appears when you first run LabVIEW (the window with tips and the buttons for New VI, Open VI, Search Examples, etc.)
For more information, read this article in the NI KnowledgeBase.
TF False
ignoreHelpAndProjDirs Set to True to ignore Help and Project directories - only built-in functions will remain on menus. TF False
independentImageDepth There's an article in the NI KnowledgeBase that partly explains this setting. numeric  
keepIntensityBitmap Unconfirmed. Set this value to True to make the intensity graph hold on to its calculated bitmap after redrawing. This speeds up redrawing for the intensity graph when it needs to update without any data change (e.g. moved window uncovered part of the intensity graph). TF False
lazyUpdateClipboard I could not confirm the following on my system when I tested it with the clipbrd.exe utility, but here's some info I received on this entry.
Indicates that LabVIEW does not really update the external clipboard whenever the user does a copy or cut operation but rather only updates its internal clipboard. When a user does paste in another application and that application uses the standard OS clipboard functions, the OS informs LabVIEW through an event that the clipboard contents needs to be updated and LabVIEW then does convert its internal data to the OS dependant standard data as required. This could be a problem if an external application uses low level/undocumented functions to access the clipboard contents.
TF True?
LVdebugKeys Enables some special LabVIEW key combinations (Ctrl + Shift + [H, W]) to open up special monitor screens to view different internal settings in LabVIEW. Information displayed is probably not very useful to someone not familiar with developing LabVIEW itself. The monitors even allow modifications of some internal LabVIEW states which will definitely crash your system if you don't know exactly what you are doing. TF False
massCompCache Unconfirmed. Indicates the number of independent hierarchies to keep in memory during a mass compile operation. This speeds up the loading of progressive VIs because most of the common sub-VIs are already in memory. numeric  
massCompLog Set to True to write a log to <lvdir>\masscomp.txt when mass compiling. TF False
memoryChecking When set to True, LabVIEW internally does extra checks to its memory management consistency whenever memory is allocated and deallocated and probably resized. This of course slows down LabVIEW tremendously and therefore is only useful to the LabVIEW developers as a user can not do much about eventual error asserts anyhow. TF False
moreColors Unconfirmed. If set to False seems to limit the number of colors to 16.
On the Sun platform, this is an option on the Preferences dialog, so this setting is also mentioned in the Colors section.
TF True
mutateToPeriodDecimalPoint When upgrading a VI from earlier versions and this setting is enabled, LabVIEW will insert "%.;" at the beginning of all format strings for all string functions which accept a format specifier input.
0 means do not modify. (Default value)
1 means modify.
2 means LabVIEW should creates a text file where it writes about any modification it does.

(I could not confirm value 2. If someone can make it work and provide a path/filename it would be most appreciated.)

nodeBreakPointMenuItem Set to True to add "Set Breakpoint" menu item to node pop-up menus. This is not the same as the red execution breakpoint. When selected, it appears to trigger a hard debugger break within LV. Probably only useful for the LV development team. TF False
RecentFiles.maxNum Maximum number of Recently Opened Files to list in the File menu. numeric 10
RecentFiles.showFullPath Set to True to show full paths of Recently Opened Files in menu.
The default is False, but LV will automatically show full paths if two or more recent files have the same name with different paths.
TF Auto
RegisterExtensions Set to False to prevent LabVIEW from re-registering the .VI, .VIT, .CTL, and .LLB extensions to itself upon load.
The default is True for the development environment and False for a built executable.
TF Auto
saveAsVHDLMenuItem Setting this to True adds "Save As VHDL..." to the File menu.
This writes a wannabee VHDL description of the current VI to a file. This is not working correctly yet but indicates that NI is trying to create a LabVIEW version which will eventually create VHDL files to be compiled by an external VHDL compiler and be downloaded to an ASIC (Application Specific IC).
TF False
saveFloaterLocations Set to False to prevent saving screen locations of open palettes on exit. Note any existing menu.n settings will not be removed so you can have LV always open the same palettes on launch, even if they were closed upon last exit. TF True
scrollGraphCursors Setting this value False prevents a graph from scrolling when you drag a cursor beyond the bounds of the graph. TF True
scrollingStripCharts Setting this value to True appears to speed up the redrawing of a scrolling strip chart by scrolling the existing bitmap and drawing only the new part rather than redrawing it completely. TF False
serialDevices The information below applies to Windows only.

In the default state, LabVIEW can address up to 10 serial ports and 4 parallel ports using the serial VIs. The default entry is:
serialDevices="COM1; COM2; COM3; COM4; COM5; COM6; COM7; COM8; COM9; \\.\COM10; LPT1; LPT2; LPT3; LPT4"

To address additional serial ports, such as when an expansion card is added, you must add an entry to tell LabVIEW how to address the additional ports. For example, to set it to support up to COM16, you would add the following line to labview.ini:
serialDevices="COM1; COM2; COM3; COM4; COM5; COM6; COM7; COM8; COM9; \\.\COM10; \\.\COM11; \\.\COM12; \\.\COM13; \\.\COM14; \\.\COM15; \\.\COM16; LPT1; LPT2;"

The above should appear as a single line in your configuration file. Names of COM ports greater than COM9 should begin with "\\.\"

For more information, and for info on other platforms, read this article in the NI KnowledgeBase.

showInplaceMenuItem Set to True to add "Show Inplace Set" to the popup menu you get when you right-click on a diagram terminal. Selecting this menu item makes the terminal, and all other terminals sharing the same data inplace, blink together. Pop up again and select "Hide Inplace Set" before moving to another set of terminals, since it won't automatically stop blinking the first set before showing a new one. TF False
silentDatalogConvert Set to True to suppress dialog when opening an older format datalog file. TF False
simplePopups Set to True and the menubar menus will mimic built-executable menus. TF False
smoothGraphMarkers When set to true, the cursors that have Allow Drag turned off will draw into the offscreen buffer with the plots, rather than over the plots. This is also dependent on having smooth updates turned on either in the preferences or on that particular graph. This won't do anything unless you have at least LV5.1. TF False
sparcV8 Unconfirmed. Sun platform only. Set this option to only use sparcV8 code. TF  
syncVisa In LabVIEW, any calls to VISARead or VISAWrite are converted to the VISA Driver calls viReadAsync and viWriteAsync. This allows the VISA driver to work on the request without blocking LV from executing. However, under some GPIB controllers, there is no interrupt mechanism from the low level GPIB driver to tell LV when the read or write is complete. This means that to implement the Async call, LV must spawn a thread and have it poll the low level GPIB driver. Currently, the polling time is 500ms. This is why you see such slow transfers under LV with some adapter cards.
Setting this option to True makes LV use the viRead and viWrite VISA calls. This means LV will block during VISA calls, but your GPIB throughput will be much faster.

Note this option is no longer present in LV versions 6.0.2 and above. In these versions, you must pop up on each VISA read/write function and select "Do I/O Synchronously".

tileUpDown Set to True to assign ctrl-T hotkey to Tile Up and Down. TF False
useDefaultTimer Set to False to increase LabVIEW's timer functions to 1ms resolution. TF varies
useNativeColorPicker Unconfirmed. Mac only. Use the Mac color selection dialog instead of the LabVIEW one. TF False
useNewPrintHeader Set to False to use the old style print header when printing out VI documentation. The old style did not show the "Printed on <today's date>" line. TF True
useTaskBar PC only? Set to False so that VI windows will not be shown individually on the Task Bar. TF True
useWindowMenuBars Set to False to turn off menubars on all VI windows. TF True