Canderous, T3-M4, HK-47 - Traveling with the Exile
Jolee - Being a cranky old hermit on Rakata Prime. He figured he may as well settle down there and explore the land.
Zaalbar - Returned to Kashyyyk and became the Chieftain
Bastila (prior to being seen on Telos) - Taking up moisture farming on Tatooine. The Sith Lords at the time cared less about moisture farming
Carth (prior to being seen on Telos) - Asked the Exile to go to Telos, and then wound up going on a "search pattern" which took so long the Exile was able to reunite 3 Jedi Masters on Dantooine. Eventually Carth gives up on the search pattern and just goes to Telos, getting there later than Darth Nihilus
Mission - Either A) getting into trouble and getting back out of it, or B) being a cantina dancer
Juhani - Selling Gizka after giving up the search for Belaya
And that's just the party members. I could try figuring out what some others were doing (ie, Yuthura Ban, Motta the Hutt, et. al.), but I'm doing that now