blk

My usual ride is about 25-30 miles, 5 or 6 times a week. The longest I've gone is a slow metric. Yesterday my girlfriend broke up with so I decided to cope by riding. I ended up doing 100 and change, but my knees started seriously hurting around 40 miles. They still hurt today and I walk stiffly. Hard to tell where the pain is coming from. I don't stretch before riding...does this sound like a stretching issue or a bike fit issue?

10 Wheels

Raise your saddle up.

sabazel

This sounds like a classic overuse injury. RICE your knees and don't ride for a few days. Your tendons are flaring up and are basically saying "WTF did you do to us??" I've been there, it's frustrating, but you need to take it easy so you don't make it worse.

LAE

If you can tell where the pain is coming from you can usually isolate the injury and the muscle causing it. Then you can work on getting better and preventing it happening again (for the most part). Try a few different leg extensions, try rotating the leg when full extended, try extending against light resistance etc etc. Also just noting things through out the day I.E when does it hurt when walking? does it hurt as you begin to sit down/stand up in a chair?

However with all that being said, its as Sabazel said and more likely overuse. Especially considering it starts at around 40miles and not as soon as a specific action is taken.