Uaaaaugh, MojoPack sounds just.. Horrible. Not the service, but the name itself. MojoPack. Ugh.

I KNOW, its like a rastafarian lunchbox

Ba-dump tish!

I tried to play Fallout from my flash drive once. I encountered no registry problems (given the drive letter must be the same of the installation), but the game loaded and ran very very very very very slowly :-(

There we go. Flash drives are insanely slow.

Don't forget there are huge variations in speed between different devices - especially in write speeds, but also in read speeds. Cheap flash drives are almost always very slow, 4-5 MB/s or maybe slower. There are much faster drives available, but they are rarer and more expensive. You can get up to ~20 MB/s which appears to be max for the USB mass storage device class. For comparison, internal hard drives in desktop computers were typically 70-100 MB/s last time I checked. (Sequential read speeds)

I regularly play games and emulators off of a flash drive. I'm currently playing Hitman 2 and Morrowind this way on my work pc during lunch. I install the game and then use a nocd patch on them. I've only done this on a few games, but I haven't had any problems, yet.

I have played Ghost Recon on multiple computers cause I had a recent LAN party and we had no trouble getting set up.

If I ever get an admin job as a clerk, I'm so bringing Jagged Alliance to my work place via a thumbdrive

Yes, that's another point. Some USB drives grat more read and write speeds than others.
May speed also depend on the USB drive capacity and free space?

No, drive space doesn't make a difference.

Mmm, I see.

An interesting development: (this may be old news to some)
You can now get flash drives with an eSATA interface or with both eSATA and USB. This basically means that the maximum theoretical speed is 300 MB/s. (If you're lucky enough to have a computer with an eSATA interface) I don't think that we'll see drives that fast just yet, but at least these drives aren't limited by USB 2.0's measly ~20 MB/s.
Comparison with benchmarks here. The fastest ones get 80 MB/s on the sequential read test and 50 MB/s on sequential write. Too bad they didn't test random access writes though - only reads.

Is there any way that i can get shortcuts to work on a USB flash drive. whenever I try the shortcuts on the computer I originally downloaded the game on it worked but on other computers the shortcuts don't work. Is there any way I can get past this issue?

Sure, use bat files.

Windows shortcuts store the complete path, including the drive letter. When you mount the drive in another computer, the drive letter probably changes, thus breaking the shortcut.