Andyg, you can use (install) a program in the USB disk.
The only limitation is if the program allows or not this. For instance, an antivirus won't be able to run from the USB disk. Other programs, especially the simple ones, the ones which does not use Windows Registry to store configuration (for instance) could be installed in the USB disk.
What do you have to do?
Take the setup.exe file of the program, run and choose 'custom installation' and choose a folder into the USB disk. If it allows and works, great!, your program is installed there.
The access to an USB drive will be considerably slower than the normal HDD. But, never mind, you don't use that programs very often.
But, what I can't see is that you will speed up your system...
You won't...
You will only have more free disk space. If your internal HDD is small, very small, ok you will improve performance. Otherwise, I can't see a way to speed up normal operation. You can speed up defragmentation, etc. but, normal operation, I can't see a way...
You can always remove programs from the startup and run them when you need/want.
But, in this case, post real examples of your system. We can help you
