Mine actually leaked just a tiny bit where the roof met the front windshield and side windows on both sides. The previous owner didn't really take time to address the seals, so I have started doing so. I've been using silicone grease which I got from Honda (use the part number in the information below) to care for the seals which the top rests on.
http://www.teamdelsol.com/technical/...ce/default.asp
For the other seals like where the windows touch, buy silicone spray from the Honda dealership as well. I did and it works very well in reconditioning the seals and dries so it doesn't smear the windows.
You'll probably be out like $20 for both together, but better than $200 plus mine hasn't leaked since. Give that a shot first and see if it takes care of your problems.