I also have an issue with the mouse. At the moment im using a Logitech G9 laser mouse and none of the buttons work but i can use it to look around. Im gonna have to dig out an old mouse to play it, i hope there is a fix for this because it'll be a pain to keep swapping mice.

Maybe a stupid question, but have you tried binding the buttons to actions? When I loaded it up, none of the mouse buttons were bound to any actions under Options->Mouse->Left Button, Right Button, Middle Button. I set my LMB to fire and my RMB to tractor beam (which I don't seem to have yet, so I don't know if this is a useful action). I also set my movement controls to WASD rather than the arrow keys.

Star man! I checked out the button bindings and sure enough none of them were assigned to anything at all. Im quite surprised the controls arent set for the mouse by default. Anyway, thanks dude.

I also have been having this problem with the mouse. I can look around, but not use any of the buttons. I am using an Intellimouse Explorer 3.0 with updated drivers. I have also set the controls for the mouse in game, with LMB being Fire, RMB being double jump, etc. Looking around works, but none of the buttons do their function.

I just started a support ticket for this exact issue Monday (07/06/2009) and sent along my DXDiag.txt file. I have a Logitech dual optical. Through a little Google Searching, I found that it might be that USB mice weren't supported very well with this game. I haven't tried a PS2 to USB adapter yet (just haven't had time to try it), but if someone has success with this method, please post back here.

I have the mouse issue too. In the options menu, the mouse does not seem to work at all, I am unable to assign the mouse buttons there. I have tried making changes in the default config file too, but that does not work either. I have a USB optical mouse.

I have the same problem. I just got a simple USB Labtec mouse.
A temporaly solution if you reconfigure "E" as fire button.

I had the same problem too but the solution is actually very simple. Just highlight the mousebutton that needs assigning and use the left and arrow keys to assign the action.

YES!!! The previous poster is right. using the arrow keys you can scroll through a list of options over what you want to assign the mouse buttons. My problem is solved. Yipee!

Mouse won't work to look around.
Mouselook is On and the mouselook key doesn't do anything either. maybe a Windows 7 problem?

Got a mouse problem as well.
I have a Logitech G9 laser mouse.
I get some really bad mouse stuttering\lag. When moving\looking up or down.
If I set the mouse smoothing to max then it stutters less, but still stutters a lot.
Also if I move the mouse very slow, in-game it won't move at all.

I'm having an identical problem. Stuttering mouse. I don't want to look/shoot with the keyboard, but it's starting to seem like the mouse isn't going to cut it.

For mouse look not working at all:
Make sure the "Sensitivity" bar is not at its minimum. If it is, then it wont work.

For stuttering and lag:
Put the "Smooth Mouse" bar all the way down to nothing, then move it up 5-6 times.

Hope this helps.