From what I have learned (BS in Exercise Science)...
you can't stretch too much, but you can become too flexible. It is this flexibilty that can cause a problem. To gain flexibility you are giving up stability (you usually see this in joints). This is why you see a lot of ankle, knee, or hip injuries with dancers (ballet usually). They have stretched so much that their joints no longer have any support so they can't stand up to any unusual pressure.
But as far as stretching, you can do that as often as you like during a day. The important thing is to be really warmed up first. Stretching cold won't increase flexibilty. You should also hold a stretch between 15 adn 30 seconds (depending on who you talk to). Anything less than 15 won't do you any good, anything more than 30 is just wasting time.
The whole "pain" and "discomfort" line is a hard one to gage. You just have to listen to your body. If you pull something, figure you went to far! Also, it is not good to try to stretch something you have pulled, you are usually only making it worse. Let it heal completly, then go back to stretching.
I am at work and have to run, but we had a good stretching thread in the Taekwondo area going awhile back, maybe do a search and see what you can find.