I'm not using a flash drive, but I've started a separate partition (actually a file being treated as a drive via ImDisk) for portable apps -- the idea here is that my inevitable OS-reinstall can be made much less time-consuming because in theory, I shouldn't have to muck w/ at least the partition with the portable apps (as a bonus, I can have multiple OS installations use the same portable apps).
I started with the just-mentioned Lupo Pensuite and have been carving away things from its Apps directory that I don't use and have been adding updates and new apps to its Plus directory.
The file-being-treated-as-an-image is about 2GB in size so I could move the content to a flash drive at some point -- my current usage comes in at around 1.7GB and WindirStat (portable of course!) tells me that the big users of space are:
- Chrome - about 500MB (> 400MB is in a Data folder)
- OpenOfficePortable - about 250MB
- JDK - about 160MB
- emacs - about 130MB
- GnuCash - about 100MB
- Firefox - about 70MB
As to what I've found useful , that would be (apart from what's mentioned above) :
- Find and Run Robot (and some of its plugins)
- Freemind (though I modified its startup batch file -- their FAQ gives some tips)
- Icons From File
- JFileSync (though I modified its startup batch file)
- Nirsoft Utilities (as in, many things from there)
- Sysinternals Suite
- TapTap Hotkey Extender
- TaskSwitch XP
- The Regex Coach
- TicToc Title
- Universal Extractor
On a side note, I'm hoping some of the up-and-coming file association managing tools will come out of development states (and get tested) and I hope to come across some good app/system to manage keeping apps up-to-date (looks like I should take a look at: FreewareUpdater).
 I made separate categories in ASuite for things that I'm pretty sure I'll be using (based on recent experience or gut feeling), things I'm trying, things that have problems, etc. -- what I mentioned here is from what I'm sure I'll be using.
 Some of these are specific portable versions and some just worked as is