Since this thread is still kinda going, I'll add my two cents:
With or without emacs, the ctrl key is useful for tons of stuff on linux or windows: copy, cut, paste, find, close, quit... I use this stuff constantly. So as others have suggested, I want that near the spacebar so I can use my thumb. And that's how it is by default on a mac, where all that stuff uses the cmd key:
[ctrl] [alt] [cmd] [spacebar]
So, I use a mac keyboard on my linux box, and set up the cmd key as a second ctrl key (In Ubuntu Lucid: Keyboard Prefs > Layouts > Options > Alt/Win Key Behavior > Control is mapped to Win keys (and the usual Ctrl keys))
[ctrl] [alt] [ctrl] [spacebar]
Other benefits:
* When I need to use a mac sometimes, cut/paste/etc are all in the same place I'm used to.
* ctrl+tab (with the real ctrl key) still moves through tabs for browsers and other apps, on both platforms.
The drawback to this plan is that the alt key has moved to the left, so the alt+tab command (which I use for window switching) no longer matches the mac equivalent cmd+tab. But I can still hit it with my thumb, and it's still, to me, a far lesser evil than destroying my pinky. Yeah, I know I could just make ctrl+tab the window switcher, but then the real ctrl key doesn't work for tab switching. Besides, with apps moving into the browser, the window/tab navigational strategies are gonna be in flux for a while -- but the basics like cut/paste aren't going anywhere, so I want them locked down. Under my thumb.
(Of course, if you wanted to use emacs on a mac, I guess you'd be back at square one...)