I prefer a bolt-on because it is so much easier to replace the neck if you run into problems down the road, or just feel like changing something.
A neck through offers some strong theoretical advantages, especially with the longer necks of basses.
There are potential problems with set in necks - a glued joint doesn't seem that great to me - but there are lots of great guitars with set necks:  PRS, Gibsons, etc.  Actually, the PRS neck joint may be a "bolt in" instead of a "bolt on".  
There's some interesting info on the Taylor site about how their neck joint works.  Tons of contact area, attachment screws designed to provide for adjustment, etc.
Chip