That brings up a good question. Right now, I compile all my programs for a specific path. While they *could* work in a different place, most look for additional files within that path. For example, FBReader looks for all of it's icons withing /installedpath/share. So I had to release a version that works with compact flash cards and also mmc/sd.
However, I could setup the initial run script so that it makes a symbolic link somewhere on the root file system to wherever you have the program copied. I am hesitant to touch the root file system with a script though. I haven't yet, and I'm not sure if I want to before the unbricking option is available.