Just upgraded to Debian unstable (good idea?). Everything appears ok, apart from my X configuration is lost. X no longer starts during bootup, and the progs xf86config and XF86Setup are not available. Also startx and X are unrecognised commands.

Congratulations! You're now the proud owner of an X4-based system. You may need to make sure that you have the right packages installed (try "aptitude" if you have it installed... I'm not sure if it's the right tool for unstable now, though).