We went during Jersey week in 2004 and the week leading up to Columbus Day in 2005. I'd give the slight edge to Jersey week- the resorts seemed more full then. Our longest wait in line during Jersey week was 40 minutes at 1 pm for Kilimanjaro Safari at AK, and 35 minutes at about 11 am for the Great Movie Ride at MGM.
The week of Columbus Day, we didn't ever have to wait longer than 20 minutes in line- the line for Soarin' was posted at 60 minutes, though, and the FPs were gone by the time we got to them (around 3 pm). We decided not to wait that long.
Weather-wise, Jersey week was much nicer- no rain and much less humid. Columbus week was extremely humid- very uncomfortable. And it rained every single day for at least 1/2 hour or so.