On a reasonable computer (aka: mine :P) the position of these keys is pretty much irrelevant, because I can remap any to have the behavior of the others. In all configurations I end up with these three keys, and the only interesting question is what those keys do. Windows, traditionally lacking the third key, uses ctrl for application-level commands and alt for menus. Linux uses ctrl (and alt, but not as often) for text-editing (readline) commands, effectively preventing any application-level commands. OS X neatly sidesteps the collision by using their meta key for their applications and leaving ctrl and alt alone for the terminal.
Linux GUIs, unfortunately, seem to be following Windows, which means you’re never quite sure whether ctl+a will jump to the beginning of the current line (the traditional behavior) or highlight your entire document (from Windows; pretty universally regarded as a mistake because bumping it then typing wipes out everything). LogJam is stuck using ctl+alt+key for most of its commands (GTK even steals ctl+shift+[a-f] for Unicode characters) and that’s just awful.