[color:"orange"]let the player choose between quests, only some of which can be completed before something else happens.[/color]

If there are going to be limits on which quests can be done (which seems likely), it should be setup in-game that they conflict, rather than some arbitrary or artificial limit.

The easiest way to do this would be to have conflicting goals (steal or guard someone's treasure), but that is so simplistic too much of it would detract from the plot. I liked in DD for the two guys in Verdistis that wanted you to take out the other, that you could tell them they deserved each other and refuse both quests. Only slightly more subtle, there could be opposing factions; helping one faction would drop your reputation enough with the other that they would refuse to deal with you (unless they really needed you, as in Yojimbo / A Fistful of Dollars <img src="/ubbthreads/images/graemlins/biggrin.gif" alt="" /> ).

The choices you make could also change situations so some quests are no longer available. Say there is a town where the only known feasible trade route is cut off by a group of monsters too large for the local military to deal with directly. Only one merchant has a consistent supply of goods, which consequently are very over-priced. The military wants the trade route cleared and the merchant wants a body guard, as some take exception to his pricing practices. If you help the merchant, a military mage could track you to the hidden teleporter pad he uses. Rather than accept your help, the military could then just use the teleporter pad to get behind the enemy lines and make a surprise attack. If you help the military and clear the trade route, the merchant looses his monopoly and his source of power, and could be arrested or lynched; either way he would no longer need a body guard.

You could also have a Sophie's Choice style dilemma (minus the personal attachment), with a town being evacuated before an invasion. The military is better able to defend themselves, but without your help they don't expect to be able to hold out for long. The civilians are being evacuated through relatively safe territory; a few wounded soldiers and farmers with pitchforks can deal with the odd monster, but any concerted attack would do a lot of damage. You can either stay and help a small strong group that will definitely be attacked, but who might be able to defend themselves if they are lucky, or help a large weak group that probably will not be attacked, but if they were the results could be devastating.