Besides Team Fortress 2, the Half Life series, and Portal. I'm going to load Xubuntu on my other HDD soon, and I want to have some games to play off the bat.
FTL has gotten a native linux port also Starbound will be available for linux on launch
Bastion is great if you haven't played it yet, that's basically required reading for a gamer IMO Dota 2 has been ported, and is free, but if you're not already into MOBAs it will be a time investment learning about it. If you haven't played Psychonauts yet, grab that. I recommend a controller for this one, USB 360 controllers are godly and work great in Linux. I also second the suggestion of Dwarf Fortress, it won't tell you outright but you'll need ia32-libs for it to work right if you're on x64.
Iesabel, http://iesabel.com/ Hack-n-slash rpg with multiplayer.
Lone Survivor and Minecraft are the only linux games I've frequented. Check out Wine, you can play a large amount of Windows games at native speed.