Exact same situation here, just got my 4GB card. I have started sorting my roms as well, I have about 40G between NES, SNES, GB, NG, GBA (<fingers crossed in hope>). If you are in windows, do as stated above. In linux you can do the following:
for i in *.rom; do zip $i $i.zip; done
which produces foo.rom.zip bar.rom.zip baz.rom.zip etc
I also have a nice shell script that takes a large directory of roms and creates 27 subdirs (A B C ... X Y Z 0) and sorts every file into the appropriate directory, then symlinks them all into another subdir named All. This accomodates emulators that only support one rom dir (visualboyadvance) and emulators that crash/freeze if there are too many roms in one dir (zsnes). I will post it when I get home.