I think some are still there, but many are gone as well. Proof:
Ricky Blitt: Hasn't written an episode since season 2, production-wise. Went on to create "The Winner".
Neil Goldman/Garrett Donovan: Ditto. Went on to "Scrubs".
Gary Janetti: Last work was on Stewie Griffin: The Untold Story. Went to "Will & Grace".
Matt Weitzman/Mike Barker: Last wrote during season 3. Now on "American Dad", obviously.
Craig Hoffman: Last one was during season 2. Not sure what he did after that, other than "Endgame", a made-for-TV movie.
Bobby Bowman: Only wrote one episode in season 2. Went to "Yes, Dear" and "My Name is Earl".
Dave Collard/Ken Goin: Season 3 was the latest. Went on to "Tripping the Rift".
Jim Bernstein/Michael Shipley: Only one season 3 episode (technically season 2 in production order). Briefly worked on season 4 before going to a variety of shows like "Oliver Beene", "My Name is Earl", and eventually "American Dad".
Alex Barnow/Mark Firek: Season 3 was their one and only. Now (or previously, I think) on "Til Death".
Allison Adler: Ditto. Went to "Still Standing", "Life As We Know It", "Chuck", etc.
Daniel Palladino: Double ditto. Went to "Gilmore Girls".
Gene Laufenberg: Last one was at the very start of season 4. Went to "Living With Fran" (yeah, I haven't heard of it either).
New writers for season 4 and onward: Patrick Henry
Alec Sulkin/Wellesley Wild
Patrick Meighan
Tom Devanney
John Viener
Matt Fleckenstein
Kirker Butler
Michael Rowe
Tom Maxwell/Don Woodward
Cherry Chevapravatdumrong
David A. Goodman
Andrew Goldberg
Brian Scully
Alex Carter
Richard Appel
The directors have shuffled, too. There are still some veterans on the show like Peter Shin, Pete Michels, Dan Povenmire, and John Holmquist (who did one episode in season 2 before returning with "Airport '07"), but these people, AFAIK, are gone:
Michael Dante DiMartino: Went to "Mission Hill", "King of the Hill", and most notably, "Avatar".
Roy Allen Smith: Went to, um, "LeapFrog". Never heard of it.
Monte Young: Did various episodes of "The Oblongs", "King of the Hill", and "ChalkZone". Not sure what he's doing now.
Neil Affleck: I think he was working on FG and Simpsons simultaneously, though I could be wrong. Went on to "Miss Spider's Sunny Patch Friends".
Jeff Myers: Jumped ship for "King of the Hill". Though interestingly, there was an eight year gap between directing jobs on that show (2001 to 2009).
Bob Jacques: Went on to "The Oblongs" (briefly) and "My Life as a Teenage Robot" before working on some more Spumco stuff, I assume at Carbunkle.
Jack Dyer: Went to "The Oblongs". Also apparently did some animation timing for "The Simpsons".
Swinton Scott: A bunch of stuff after FG: "God, the Devil and Bob", "Futurama", "The Batman", "Camp Lazlo", "What's New Scooby Doo".
Gavin Dell: Worked on the infamous Larry Doyle Looney Tunes shorts.
Scott Wood: Who knows what he's doing now.
Glen Hill: Ditto. FG seems to be the latest thing listed.
Bert Ring: Went to work on "Curious George" and "Tak".
Rob Renzetti: Now doing a bunch of work for Nick and CN series.
Brian Hogan: Went to "Billy & Mandy", "Baby Blues", and "The Batman".