Seat height and gear choice.

You can find references to correct seat height pretty easily. Just do a few searches. Knee pain is often related to it. (You might do some reading up on "iliotibial band syndrome," too.)

Choose the easier gear and a faster cadence, not the harder gear and a slower cadence. You want to be spinning, not pushing. Once you're OK like that, and the knee isn't hurting, you can start increasing resistance. Every time I'm off the bike for more than a few weeks, I get back on by spinning for a few days before starting to push again--for exactly this reason. My knees get injured if I don't. I also start by commuting one way for a few days instead of making the whole round trip: Home to work, leave the bike there overnight. Work to home the next day. Repeat a few times. Then start the round trip the following week.

You know how a chain is only as strong as the weakest link? You've got some really teeny muscles in there.