I am not an expert here (just a member), but I found this list of mobility warm up exercises by Mike Robertson and Eric Cressey on bad knees in one of their threads at t-nation.
Try these and let us know how you feel after doing these. This is probably what you need to get you going and more mobile. Do them in order. If there are any you don't know, just go to google and type in its name in between " " to find your results faster and see pictures/descriptions on how to do these. As far as reps go for each one of these, I am not the person to ask. One of the experts on here may be able to help you with that. For me, I usually make up my own reps from 5-10.
people with knee problems...
Birddog
Calf Stretch
Supine Bridge
Hip Corrections
TESTOSTERONE NATION (find the letter Q)
High Knee Walks
Pull-Back Butt Kicks
Mini-Band Side Steps
Cradle Walks
Single Leg RDL (more for glute medius recruitment than hamstring stretch)
Reverse Warrior Lunge w/Twist
Walking Spiderman
Alternating Lateral Lunge
Squat-to-Stand