I have gentoo installed and X running finally, with my usb intellimouse explorer 3.
I have some APM modules installed, however I'm not sure they work.
Anyhow, here is the weird part, which is a real nuisance.
If I do shutdown now -h, linux will run its shutdown procedure, then say 'Powerdown'. And it just stops there. So I click the button to power it off (because I don't know how to make it turn itself off yet). Now, when I restart the machine, my usb mouse is no longer detected at startup (you can see the infrared flash and stay on when you boot, while it's doing memtest and post stuff, even before choosing an OS to run). Whether I then boot to windows or linux, there is no mouse at all.
The only way I can get the mouse back, is to boot up off a redhat 9 disc I have (not installed), then let it run up to about the point where it asks if you want to check the disk, and whalla, the mouse is now detected again and I can ctl-alt-del to reboot and the mouse is OK again.
This only happens when I actually turn off the machine. If I do shutdown now -r to reboot, it still works fine.
I hope someone can help me with this, because it's a right pain in the backend. (It would also be good if someone has some ideas about the APM stuff!!)

The USB modules may not be loading at boot, this will stop your usb mouse from working.

The usb modules load during bootup, they are in /etc/modules.autoload.
I didn't have the apm module loaded, so I put that in also, but it didn't make any difference either.