Do something like the bike to get your knees warm first, taking in mind that you are just there to warm up not get a cardio workout. And +1 all those videos.
Another thing, if usually the two days between my day 3 and my day 1 are enough to get my knees stiff (I squat three times a week on my program). I find a am pretty tight and things feel wrong until my third or fourth set. It isn't uncommon at all for me to have some minor pain at 135 or 225 and then by the time I work up to my 300+ sets everything feels gravy. There have been a few nights where I almost called it because of knee pain worries on set two or three and found it was all gone after a few sets, and I mean everything felt great, not numb.
As far as hamstrings, I know one thing Mark Rippetoe recommends for people with tightness is to go to the bottom of a squat, put your fingers under your feet, and then straightening your legs back out, raising your ass, and staying bent with a flat back, then holding this for thirty seconds. Doing this each day when you get out of the shower (everything is nice and warm) well have your hams a lot more flexible in a short amount of time. Just make sure no one walks in your stretching, lol. They will be scarred for life. The idea is to eventually get to where you can straighten your legs completely while keeping bent over still on your fingers. Worked well for me.