What have you guys done to fix water leaks coming from the rear quarter windows? Should I lift up the flap of the seal and apply a bead of silicone? Should I replace the window seal?

The stuff that looks like condensation isn't actually wet, I don't know what it is but it's dry solids. You can see the dirty trails where water is running.

 

That's a pretty good leak.
My vote,window seal.