This is very, very different from player to player.
There are great guitarists who can't play the same thing twice to save their lives (Jeff Beck, anyone?) and there are those who play their parts in a very diciplined way, everything will sound essentially the same, time after time.
Usually, the "we are a live band" high-principle guys look at studio recording as if it were figure skating: they have to make it through the song, every time, all the time, and not fuck up once, in order to assume that nice smiling pose when the music stops.
90% of these guys can be talked into it by example ("Guys, Pantera, Steve Vai and King's X all overdub, and they're all amazing live acts") or by demonstration (track several guitars, play back with just one, and then add all of them). For the rest, you just have to make do with what they allow you, with stereo room mics, splits, multiple amps like Fibes said, or whatever. Also, if they plan to cut it with one guitar, the bass needs to be made absolutely huge to help it achieve the weight and size.
My method for tracking good rythm guitar overdubs.... Ok, go ahead and shoot me, but I found the "loop record" method yields great results - it only works on a DAW of course. Sort of cheating, but notice I don't give a shit. Music production is about results.
You set up a section, say, 8 bars of a verse, and set it to loop in your DAW (assuming you track on a DAW, or you are SOL).
Hit record and let it loop. Have the guitar player play the riff over and over. After a couple of laps, he will start getting into the groove, and because the loop repeats perfectly every time, he will hopefully find the pocket for this particular section pretty quickly.
If you do a section, stop, and start over, every time he starts over he will spend a few seconds adjusting to the groove, and the end part will usually be better than the beginning. With the loop method, the guitarist will be up-and-running when the loop starts over, and the beginning is going to sound better right off the bat.
The added bonus is that when the guitarist has played the loop 5 or 6 times over, he will have found the pocket so well that there will likely be two or more takes that are good. Presto - there's your overdub!