I think what's best to put on caps depends on your physical keyboard.
At home I type on a Kinesis Ergo Elan where my ctrl keys are under my thumbs, along with 2*alt, space, enter, backspace, delete, pgup, pgdn, home and end; the rest of the keyboard is fairly normally laid out, except the board is split.
With the ctrl keys ready at hand, it really makes the most sense to put escape on caps lock (and caps lock on esc, for the few times I need it). Even if you're an emacser, hey... it doubles as a spare "prefix alt key", and you probably ask your browser to stop what it's doing a few times every day.
On the other hand, if I'm typing on my laptop where the lower left corner key is Fn rather than ctrl (ffs...) and I can't hold down shift+ctrl with one finger, it might make sense to put ctrl on caps (such that I can hold them with a single finger). At least if you're not a vi'er, or you don't mind the escape key being further away (or have some crazy system).
What's really interesting is putting some funky key on shift+shift (yep, both shift keys). This can be done with xmodmap fairly straightforwardly; I put my compose key there. If you don't need compose, you may want to put something else (like, say, esc).