Roof rack systems...

I have used a Thule roof rack system for my Civic for a bunch of years now. It's the style that clamps down by gripping the lip where the car door closes. The problem is, this has caused a permanent break in the seal that leaks whenever it rains. Even if I remove the rack, the rubber gasket-thing has been damaged by the rack mechanism. Has anyone else experienced this?

I don't really care considering my car is so old, but with a newer car this would be a serious consideration.

I have the same style of rack system. Installed it in June. Haven't noticed a leak yet, but then again, it has to rain for it to leak.

many years ago I had this problem with yakima.  The best solution IMO is to buy the roof rails (yakima tracks) that bolt to the roof and then have a perminant rail/track system.  The other advantage to this is that its easy to take them off when not in use and the MPG/noise levels are not affected.  after the rails are installed the placement of racks with the yakima system takes about 5 min.
http://www.rei.com/product/679476/yakima-tracks-with-bolts-60-inch?preferredSku=6794760014&cm_mmc=cse_PLA-_-pla-_-product-_-6794760014&mr:trackingCode=CC83071B-81F9-DE11-BAE3-0019B9C043EB&mr:referralID=NA&mr:device=c&mr:adType=pla&mr:ad=20834090200&mr:keyword=&mr:match=&mr:filter=39033357160&msid=8pJpqDQm_dc|pcrid|20834090200|&{copy:s_kwcid}

I have had this on all my cars since 2002 and I love it!!!

Bolted to the roof??? :jaw drop

yes, I drill 7 holes in the roof on either side and bolt it down.  I have had 2 kayaks on top up to over 100mph with this system with no movement,  and run bikes into hotel portico with no damage to the car, but the bikes....

edit:  this was the first thing I did to my Mazda station wagon.  new off the lot 3 weeks prior 

I just read about something like this, although I would get it professionally installed as I'm not a mechanic! Good to know there are other options out there.