The right shoes help, too. I think of them as an investment. I've got R. Arthritis in my knees and patellofemoral syndrome in my right knee. When you go to a good store (not a lot of the chain stores you find in the mall. They usually just have teenagers or unqualified people working in them), they'll size your feet up, not just what size of shoe, but what kind of arch you have as well. They will then fit you with multiple different styles and have you walk, and even jog around in them to help determine which one is best for _you_. A good pair of shoes coupled with good form and stretching will do wonders for your knees.

I have never used a treadmill, but have always heard running on one is a lot easier than running in real life (excuse the terminology). So you ran in real life, which is harder, but you also ran a trail which has uneven surfaces which worked a whole lot more muscles and tendons than get worked on a treadmill. I would assume you would be sore. Not just knees, but in many places! Great job on the run. I would rest today, and see how you feel tomorrow. No need to push yourself too fast!

One of the biggest factors in knee pain is overstriding and heel striking. The way to overcome this is increasing your cadence. Here's a great article on the topic: http://www.runnersworld.com/running-tips/pick-beat