If you are using the GNOME desktop use gconf-editor to set /desktop/gnome/interface/gtk_key_theme to "Emacs". As far as I can tell, everything works (like I am now typing ctrl-A on firefox to go to the beginning of this line) There is also Alt, and Meta, and you can set your own keymaps in X. Actually, one of the reasons I didn't like the mac is the lack of flexibility in this area (like re-mapping ctrl and caps lock…
Cocoa by default already has some of the Emacs-style keyboard shortcuts (CTRL-A/E/P/N/B/F/K/T/Y/etc), and these are partially supported in Firefox 3.0. And it looks like remapping keys for Cocoa apps is very flexible and powerful, but I haven't messed with it personally yet (though I plan to try to get things even more Emacs-like, which appears to be pretty doable).
Of course you can't beat the flexibility that's achievable in the open source desktops/window managers.