After digging around some more I found more hidden INI keys. Again, use these at your own risk.
whileLoopSharedCloneOptions=True - adds an additional context menu option to the While loop; not sure what the different options do
GenericsAreGo=True - enables the creation of generic VI's (danger!) by right-clicking a control or indicator and selecting "Generic"
ActiveXMoreContainerOptions=True - Adds "Persist State To Edit Mode" and "Destroy And Recreate When Run" to the Advanced submenu of an ActiveX container
AdvancedPlotLegendMenu=True - Adds a whole bunch of additional options to the context menu for a plot legend
EnableStrictTypedefConstantConfiguration=True - Adds a new context menu item to constants based on strict typedefs called Act as Strict Typedef Constant. Function unknown.
enableSecretPopups=True - Adds additional context menu items to custom control parts that configure how they scale with the control. Apparently some other hidden menu items are added somewhere too. (Thanks, hooovahh and Christina Rogers!)
showRunAtAnyLoopMenuItem=True - Adds a new menu item to Property and Invoke nodes labeled "Run At Any Loop". When selected, the node turns brown as if a private property or method was selected, even if none are. Function unknown.
ShowWireAddressMode=True - Adds some additional memory-related information to the context help window when you hover over a wire. Also adds a context menu item to wires called Select InPlace Signals, which likely selects wires that share a memory address. Seems like it could actually be pretty useful for optimization!
SimShowCompanionDiag=True - Adds a context menu option to the Simulation structure called "Show Companion Diagram", which toggles showing what looks like a "behind-the-scenes" block diagram for the simulation.
NEW! ShowHiddenLibraryItems=True - Shows hidden library items. (big surprise there!) So far I've only seen changes when editing a statechart library, but it seems most of the items in a statechart library are hidden, so it reveals a lot.
There's also some more whose functions I'm not sure of (but look interesting) such as TotallySecretAndPrivateMSNCompanionDiagram, and growSubVI.enabled (might be pretty mundane, but it's false by default and might have something to do with creating subVI's that can grow like XNodes.)
If I find any more interesting ones I'll post them here, but here's a list of every INI key loaded when LabVIEW starts, obtained by hooking the internal function that reads them: http://pastebin.com/j1iAEZXg. See here for information on finding the rest.
In the meantime, if anyone knows what any of these do, please post!