1. best characters - Farscape. Lots of great characters. B5 was Londo, G'Kar, and then a bunch of crap. Sinclair, Delenn, Garibaldi, Ivanova, the kid from Lost in Space.... I didn't really care for any of them.
2. best storyline/plot - Farscape I guess. B5 had a lot of epic going to for it, but the resolution to the main storyline was a bit underwhelming. Farscape had a great story that kept building up.
3. best setting -Farscape, Moya was more interesting than the B5 station, the uncharted territories and the galaxy in general were more interesting than the B5 universe.
4. best themes - Ehh... who cares? I guess Farscape
5. best acting - Farscape. There were some really bad actors on B5.. yeah they had a couple of great ones... but Ben Browder was the best in his role across both series.
6. best music - Kind of a tie, Farscape was cooler, but B5 had some catchy classic sci-fi theme kind of stuff going on.
7. best special effects - Farscape, Babylon 5 looked like shit, especially in the first season. Props for the forward thinking widescreen, but then again they didn't bother to render the effects for widescreen. Also the effects on DVD have some awful artifacts... Farscape's computer generated stuff wasn't utterly fantastic either, but Jim Henson muppets for the win.
8. best ending/finale - I think the B5 finale was probably better than the Farscape wrapup.
9. best overall - Farscape, B5 was great and all, but when you pit 'em head to head Farscape wins on almost every level for me.