I would say either you just didn't give your body the right nutrients before workout of you strained a muscle. Get some multi-vitamins and swig some orange juice. You're body is using a lot of what you have right now to rebuild muscle, no one likes getting sick from weakened immune system.
Ice packs followed by a good hot bath with help with the immediate problem, as well as gentle stretching (well it won't feel good as your doing it!). Since you have muscle tissue damage from working out (that's what all after workout pain is) you don't want to put too much more. Gentle stretching and massaging, however, will be good.
Before you workout get a good endurance blend. I really like these because they are set up in the 4:1 carbohydrate/protein blend that your body utilizes best to rebuild muscle. Half before and half after will keep you working out longer, and your muscles from hurting after. Plus the type made by Twin Labs (pretty cheap, you can also get most any of the stuff made for cyclists) has glutamine and lysine already in this. Sure you can go the natural way, just with food, but this will help your body maximize what it can do and leave you in the least amount of pain.