i had yakima racks on my old nissan & that worked really well. a buddy of mine has always used thule. i tihnk which ever is easier/cheaper for you should work fine. both are really solid systems.
straps thru the doors are ok if you're not going long distances, but if you're going more than say, 5 miles, i'd want racks.
i do, however, second the comment about bungees. whatever you do, get a legit set of straps to tie your board down. i'd say it's almost (or more) important as the type of rack system you choose.
I've been a big Yakima fan for as long as I've been a car-owner. They have lots of attachments for kayaks, bikes, etc. Like Thule, they have a way to anchor the crossbars to just about any vehicle.
Use either Yakima or Thule, both are great. Use the one that your local bike shop/outdoor shop carries so that they can help you match up the proper tower to your vehicle and help you install it.
With good roof racks, you can carry eight boards on your roof for a road trip, just be careful how you stack them, and use beach towels to compensate for differing rockers.
And like everybody else has said, don't skimp on straps. get the good ones and replace them when they start to look frayed. Fifteen bucks for a set of straps every couple of years beats the heck out of replacing your board and the windshield of the guy who was tailgating you.
ok, I worked in a bike shop for 6 years and know my way around a rack system. Here is some advice:
Taxi racks (soft racks, fcs, whatever) are awful. This is for... taxis, your girlfriends whip, your moms station wagon, the rental car, whatever. They are not a reliable or convent solution for every day use.
IF your car has factory racks with crossbars.. then duh, get some pads and good straps.
IF your car has factory racks without crossbars- you need something called the "rail-rider" or equivalent. This is what someone above mentioned as the $75 solution (although thats way low.... Look to pay about $50-70 for crossbars and that again for the rail rider kit), plus your pads and straps.
IF your car has a bare roof- you are in the market for a complete rack system. Several of the more expensive elements (towers, crossbars, fairing, locks, attachments) are universal fit and can be easily moved from one vehicle to another. The only thing that I had to purchase to swap my Yakima rack from an explorer to my GTI was a set of $40 Q clips. Anyways, look to spend $360-$700 for a complete rack system, depending on... how complete. Towers bars and straps wont kill you, but a couple bike trays, lock cores, fairing, etc adds up fast.
YAKIMA VS THULE- Thule makes a fine rack system, but I would personally support Yakima first because they are from Arcadia California while Thule is from Sweden. Quality wise, honestly, its a toss up. They are both great products. I have had my yakima racks on 3 vehicles over the course of about 8 years. I use them for bikes, boards, small boats, a load of 2x4's, whatever. Worth the $, just make sure you dont trade 'em in with your car!
Check fit charts at yakima.com or thule.com and make sure everything works as some vehicles require stretch kits (2 door cars) or specific parts for rain gutters (older cars). Hope this helps!