I have been fighting this battle for 7 years. First I used the silicone sealer method above, then various types of weatherstripping. What seams to work the best is some thin black weatherstripping from Van's. I first saw it when a friend of mine got it with his RV-6 kit. It compresses to very thin, and has an air pocket in the center.
I have found that this stuff is rather fragile, and you have to replace about anually. That said, it is not perfect, I usually still get a some leakage in moderate rain (yellow on the nexrad on my GPS). I have not solved the rear canopy leakage problem where the pressure inside is a little lower than outside, mostly because it does not get all the way to my passenger (my wife has not complained).
If you find something better and permanent, I want to know.