Hey man, my knees actually feel the best they have ever felt right now actually.
So, things I have noticed over the last several years, for me personally... If I stop or slack on any of my mobility, stretching, and anything rehab related I get knee pain. Actually, I will also get shoulder and back pain too.
As I have gotten stronger (and older, 32 now), I require more and more additional work outside of lifting. But recently, about 6 months ago maybe, AND last year when I first started squatting daily I got atrocious knee pain. So bad that I couldn't walk up stairs, despite stretching and all that stuff.
It took me awhile, but I started using this thing called the Rad Rod Roller...
I used that thing religiously on my quads and it makes my knees feel great. What I found for me was that my thighs would get so tight from squatting that they would pull on my tendons and ligaments in my knee AND THAT was causing my knee pain. Also, I've had issues with really tight IT bands and that will pull my patella over and cause knee pain as well. I roll my IT bands on a 6" PVC pipe to alleviate that issue.
For me, when I get pain or discomfort somewhere in my body, I have generally been able to attribute it to tightness or imbalance in my body. Finding ways to correct and/or address these issues have kept me feeling healthy and lifting heavy things.
I squat pretty narrow and ass-to-grass, with no issues. Find your natural squat motion with an empty bar and KILL the mobility. Check out that roller man, I carry that thing wth me everywhere I go.
Keep in touch man.