I think almost all of my favorite "prog" bassists have already been mentioned:
- Chris Squire
- Jon Camp
- Ray Schulman
- John Wetton
- Tony Levin
- Mick Karn
- Percy Jones
(not sure those last two count as "prog" in the proper-noun-genre sense, aka Prog Rock ...but they're certainly both quite "progressive" in the literal sense.)
Some I haven't seen mentioned (I think) are:
- whoever it was who played with the Quebec band Et Cetera in their
1976 eponymous debut album. Definitely took a cue from Ray Schulman, but just
exquisite execution and ideas. (Anybody know his/her name?)
- Matthew Gruenberg played in a band called Life On Earth (along with guitarist Reeves Gabrels) in the mid- to late-1980s after having been a founding member of the "Sarcastic Post Punk No Wave Death Disco" band The Dark (who were also pretty damn awesome). Life On Earth were like what would happen if Michael Manring, Allan Holdsworth, and David Bowie had decided to form a Peter Gabriel cover band. they'd probably be insulted if they heard me refer to them as "Prog" but eff 'em. Matt was badass.
- did anyone mention Hansford Rowe? I first heard him with Pierre Moerlin's Gong, and he's since gotten way into microtonal stuff. He, like Karn & Jones (above) seems to straddle that Prog Rock/Jazz-Fusion divide.