[color:"orange"]There should be some point where you fail... just to keep the tension up, to keep it exciting, meaningful if you do or skip the other quests (you can still do them later on).[/color]
Rather than fail, perhaps some quests could simply become tougher if you leave them too long. An enemy would have time to recruit more henchmen, build fortifications, etc. Instead of NPCs simply telling you some task is urgent, they could warn of the consequences of waiting too long (a monster wounded and driven away from a village would eventually heal, becoming tougher to kill, and might return to the village). Of course if a vampire abducts someone, you shouldn't really expect to rescue them a couple week later.
If some event is going to trigger a major change and break some open quests, then it should be obvious something will happen. I don't want to leave to do something that seems urgent, only to return and find half the villagers have left. In general you can just put off things that seem like main quests until you have completed side quests, but it is not always easy to tell the difference.
I don't really like timed quests in general, but it could make for some interesting dilemmas. Let's say you are hired by a merchant to bring a wagon train of food through monster infested territory into the city, since it was no longer safe for the farmers to make the trip. On the way back you are approached by a wounded farmer, reporting that a group of farms is under attack. You can not get there soon enough unless you leave the wagons, but with no escort the food could easily be stolen or destroyed.
If you get the wagons to the city you will be richly rewarded and welcomed as a hero, but by the time you get back to the farms there would be nobody left there to save. Perhaps you could track the monsters and rescue a few people taken as slaves, but once they found out you chose not to help as soon as you could, they wouldn't necessarily hold you in the highest regard.
If you leave the wagons and head to the farms you can take out the monsters before the defenses fail, but the wagons are lost. Perhaps there was a healer at the farm doing research on a new spell (or an old mage no longer great with practical magic, but still fine with the theory), who could reward your actions appropriately. With the food lost, however, you would be scorned by the city people. The food shortage you could have helped would get worse, which means sickness would spread easier, the military may need to withdraw from the surrounding territory to keep riots from breaking out, which in turn would allow more monsters to start showing up, further isolating the city. You would have a lot of work to do to try to get back into the city folks' good graces, possibly doing quests for the merchant who originally hired you as well as the military to avoid being tossed in jail.
