My mouse and keyboard seem to "disappear" the next time I boot into a freshly upgraded version of Xorg on Gentoo without fail.

http://forums.gentoo.org/viewtopic-t-892706-view-previous.html?sid=0560bd180d44bc6b6eb27d8454e2f31f - eccerr0r:

Xorg does an internal check that the OS doesn't (dynamic linker). They probably did this because they tend to do minute API changes that aren't ELF linkable (like saying passing a 2 means delete this window, and 1 means to create; and then the next version they swapped the meaning of the two arguments). This can't be detected by the OS (which is what revdep-rebuild does), so Xorg put some internal checks, made each binary have their own version to keep versions straight.

Quick fix if you're on generic evdev:

# emerge xorg-server xf86-input-evdev

One size fits all:

# emerge -1av $(qlist -IC x11-drivers/)