Knee Pain is a common injury in runners, especially so when distance runners are starting to increase their milage. There are many reasons for knee pain, and specific diagnosis is best carried out by a sports physio or physician. This thread is only to explain how to help prevent general knee pain from occurring, it is not for curing current problems, anyone who wants to add to it with what works for them, go right ahead.
I've suffered from knee pain for a good few months, happened first when wearing unsuitable footwear on a long, mucky, run, where my legs were slipping all over the place. Took a while to calm down to a level where I could run again, and it can flare up if I'm not careful. Ways I've found to help prevent knee pain from flaring up again include:
*Running on grass. Hard surfaces greatly increase the impact forces on the knee, concrete running is worst of all. Try running for a while on grass to see how that helps.
*No more downhills. Hate this, because my favourite thing is to run fast, down a mucky hill, but the impact forces are multiples of what they would be running on the flat. So I find if I limit my downhill running, that helps keep pain at bay a lot.
*Footwear. My trusty shoes, which I had worn for three years without issue, were withdrawn, so I had to try different pairs. I eventually settled on the updated 2011 version of my trusted brand, but still ran with pain. I eventually tracked down a pair of my old 2008 runners online, am running in them now, and the difference is immense, pain went within three runs. Make sure your footwear is suitable to your gait.
This is what helped for me, along with stretches, and strengthening exercises. A lot of runners say changing their gait from a heel strike to a mid strike helps, but I'm not really experienced in that to discuss it.