I also wanted to say thanks. I've clocked over 150hours in CW3 on Arch Linux x86_64 and it's worked great.
I do have one small bug though: the old alt-key hijacking.
If I alt-tab to change the focus to another window and then alt-tab back to CW3, the game completely stops responding to the keyboard. The mouse input is fine, the game continues to run normally, but none of the key presses are registered. However, all I have to do is hit alt again and things go straight back to normal.
EDIT:
The only issue I've run into so far is this: if you press (and release) the Alt key, then none of the keys work any more. Then if you press (and release) Alt again, then the key bindings all work once again.
I use Alt-1 through Alt-9 to switch to different workspaces on my desktop, so when I switch away from the game and switch back, I have to press Alt to get the keys to work again.
This is the exact same problem with me. I don't have this problem in any another Linux applications, but I get the exact same issue when running Photoshop under Wine. I think CW3 was originally made Windows only, so I think there's something about how Windows applications are written which causes them to hijacking the alt key after being ported to *nix.