I can name a few:
-Rich Moore, who worked on The Simpsons, The Critic, and Futurama, went on to make Wreck-It Ralph
-Seth MacFarlane, who worked on Cow and Chicken and Johnny Bravo, creator and executive producer of Family Guy and co-creator and executive producer of American Dad and The Cleveland Show, went on to make Ted, A Million Ways to Die in The West, and Ted 2
-Andrew Stanton who worked on Mighty Mouse: The New Adventures, went on to work at Pixar among which he worked on the Toy Story trilogy, A Bug's Life, Monsters Inc., and directed Finding Nemo and WALL-E
-Danny Antonucci who worked as an assistant animator on The Chipmunk Adventure, went on to create The Brothers Grunt and Ed, Edd, 'n Eddy
-Tom McGrath, who worked on Cool World, The Ren and Stimpy Show, and directed the Kablam! short Louie 'n Louie (created by Gary Baseman), went to DreamWorks to co-create the Madagascar franchise and directed MegaMind
-Lauren Faust, who worked on Powerpuff Girls, Foster's Home For Imaginary Friends, Wander Over Yonder, and created My Little Pony: Friendship Is Magic, is currently working on Medusa for Sony.
-Donovan Cook, who created 2 Stupid Dogs, went to direct Mickey, Donald, and Goofy: The 3 Musketeers and Rideshare
-Larry Doyle, a writer on The Simpsons, wrote the screenplay to Looney Tunes: Back in Action and produced 6 shorts.