My options with Zsnes were rather limited
I'm using SNES9x, see this
link. Don't know if sound differences to ZSNES/bsnes might be a problem for you?
(For uploading I used a filesize-based encoding, since I have only a 10 KB upload line.)
What do you use to encode?
K-Lite codec pack, which includes DivX. For video editing: VirtualDubMod, AviSynth and sometimes Mencoder (for converting videos to AVI, if AviSynth can't open it).
Lately I've also installed Avidemux; it's similar to VirtualDubMod, but newer.
During editing: lossless (raw video dump, Lagarith codec or Camstudio codec); final encoding: DivX in 2 passes, maximum quality or based on filesize. At some point YT seemed to have problems with XviD, so I switched.