I run Etch on a desktop PC, AMD X2 processor, 2 GB RAM, 'stock' kernel. If I let the computer idle for a few hours, sometimes when I come back the PS2 mouse clicks are no longer recognized. I can hotkey around with the keyboard normally, and the mouse pointer moves normally, but mouse clicks are not registered by anything.

The only solution I've found is Ctrl-Alt-Backspace to restart X. When I do that, mouse clicks are once again detected as normal.

I don't know if it matters, but typically when I leave the computer idle it is running pptpconfig (to establish a VPN connection to work), IceWeasel, and rdesktop (logged in to my Windows machine at work).

Try leaving the machine idling with only 2 applications and change the non-running app each time to determine which app is the culprite. If it fails, allow 1 app to be present when idling, cycle through the different app's. To make sure it's one of the app's, let it idle w/o any app open.

Thanks for the suggestion. I'll do that and go from there.