The most common cause of serious damage to sea kayaks is transporting them -- not using them. On the highway you want to protect your kayaks from damage and prevent any liability issues from their flying off your vehicle and causing damage/injury to others behind your car. Good racks are not cheap, but they are necessary part of your kayaking equipment. In addition to investing in a good rack system, take the time to learn proper techniques for tying your kayak both to your roof-rack and to the ends of your car (do both for the sake of safety, so no single failure such as a buckle or knot slipping will cause a serious problem).
If you are in the market for a new car, make sure there is a roof rack solution available before buying a new vehicle. Use Yakima or Thule rack's on-line fit guide to see what choices you have for carrying kayaks on the car of your dreams. There are some cars where the rack manufacturers may not have a solution for hauling kayaks or they limit you to only carrying one kayak. Generally after market crossbars (e.g. Yakima or Thule) are more versatile (allow more than one kayak to be carried etc.) than "factory crossbars", however if the car comes with rails (rails run along the sides of the roof from front to back) that will make it easier to install crossbars, and if you buy after market crossbars chances are they will work with your next car as long as it has similar rails. There are two types of rails that cars come with: "raised rails" (were there are gaps between the roof and the rail) and "flush rails" (no gaps). Each of these rails requires a specific rack system that only work on that type of rails. A "Normal Roof" (no rails or crossbars) requires different system which usually needs "clips" or a "fit kit" specific for that exact year and model vehicle (and some vehicles may not have even have a rack solution). Racks for "Normal Roof" are somewhat universal so you can use them on your next car as long as it doesn't have rails or factory crossbars - you'll just need to get the "fit kit" that goes with the new car.
Another thing to consider before buying a car, is can you spread the cross bars out far enough to be good for carrying a kayak? It is best to have your cross bars at least as far apart as the lenght of the kayak cockpit coaming (usually 34" - 36" for sea kayaks or river kayaks) so the tie-down straps will go in front a behind the coming. A lot of cars have fixed points where you have to put the cross bars and these fixed points are usually narrower than ideal for hauling kayaks (they are designed for hauling bikes). Raised rails are usually the most versatile for this. Some "Normal Roof" can also be versatile if the car has a long flat roof (e.g. not a compact car or one with a curved roof).
If your car didn't come with factory installed cross-bars, your first step is to choose an aftermarket cross-bar and "foot" system to attach the bars to your vehicle. For kayakers, there are two main manufacturers of roof rack cross-bars to choose from, Yakima and Thule. Both these brands have been around for decades, and both make racks to fit most cars and light trucks. Both Yakima and Thule racks are similarly priced, good quality, durable, and have a variety of accessories that fit them for carrying kayaks, bikes, skis, etc. It used to be the main difference between these two brands' of roof rack systems is that Yakima had round tubes for the cross-bars while Thule used rectangular tubes for the cross-bars. While they still make these legacy cross bars, both brand now offer aerodynamic crossbars which create less noise and give better gas mileage. If you own Beetle, Prius or other vehicle with a highly curved roof, then Yakima's round cross-bars are the way to go because the round bars allow you to rotate your cradles in order to get them to sit flush against the hull of your kayak. It's important that the kayak carrying cradles make full contact against the kayak's hull to prevent warping or other damage to your kayak. However, if your vehicle doesn't have a highly curved roof, then you'll find having your kayak cradles be free to twist around the round cross-bars is very annoying when loading your kayak because they will mis-align themselves when you try to slide your kayak forward or backward to balance it on the cross-bars. So unless your car roof is highly curved we recommend the newer aero style cross-bars.
Once you've chosen the brand of cross-bars, your next step is selecting the kayak carrying cradles and/or lift assist system for your rack. There are several good brands to choose from for kayak rack accessories: Thule, Yakima, and Malone of Maine, and Kuat. In most cases you can use any brand's kayak cradles or lift assist system on either Yakima, Thule or factory cross-bars. Which brand of kayak cradles is best has changed over the year's and also depends on how you want to carry your kayak (upright or on its side), whether you can lift the kayak on and off with brute force or need some load assisting gadget, and your budget.
As cradles without load assist go, ones that hold your kayak upright (also called vertical) are simplest to use. "J"-cradles which hold your kayak on its side require a bit more thought when tying down your kayak, however, kayaks are stiffer on their sides so there is less risk of damage or warping with "J"cradles. Carrying kayaks on their side also allows you to fit more kayaks on your roof (or a combination of kayaks and bikes) because kayaks take up less roof space when on their sides. With some cars the upright rack may limit you to just carrying one kayak whereas with "J"cradles the same car could haul two kayaks. For upright cradles we recommend ones with large surface area, good cupping around the kayak's hull, and grippy material (you can always set a towel on the cradle if you want to make it slippery in order to slide the kayak back and forth, but going down the highway grippy is good. As "J"cradles go, we recommend ones that fold down so when you aren't carrying a kayak you can park in lower garages without having to take the cradles off.
The easiest load assist/kayak cradle system to use is Thule's "Hullavator". This system includes kayak cradles that are hinged so as to drop down over the side of your vehicle allowing you to load your kayak into the cradles at waist height, get it tied to the rack while it is in the low position, and then it has hydraulic springs that lift your kayak up onto the roof with little effort. It's not cheap, but then neither are carbon graphite kayaks or visits to a chiropractor. If you can lift half the weight of your kayak, Malone makes a lower priced alternative to the Thule Hullavator that the call the "Telos" Load Assist Module. Malone's "Telos" system is designed to hangs off off the end of their "J" cradles. The Telos allows you to set the kayak in its arms at waist height and then ratchet the kayak up to roof height a step at a time by lifting one end of the kayak and then the other. Once your kayak is even with the height of your cross-bars you simply push it into Malone's "AutoLoader" or "DownLoader" "J"-Cradles. If you carry two kayaks, one Telos is all you need to get both kayaks up or down (assuming you have two sets of the "AutoLoader" or "DownLoader" "J"-Cradles). So the savings really add up vs. two Hullavators systems, and the Telos system lets you use "J"cradles whereas the Hullavator is and upright cradle system once the kayak is on the roof. Another way to only lift half the kayak at a time is to roll or slide it up from the rear of your vehicle. One systems for this is the Yakima "SweetRoll" which combine the function of the rear kayak cradles with rollers. Thule has a competing system called the "Roll Model" which separates the roller from the rear cradle, but otherwise accomplishes the same goal. A fancier version of this concept is Yakima "Showboat" which puts the roller system on a bar that slides aft while loading the kayak then tucks back in place once the kayak is in the cradles. Thule has a similar system called the "Slipstream" which slides out over the back of your vehicle and tilts down for loading. Once the kayak is strapped on you simply slide the whole system back onto the roof.
I haven't made a recent comparison of the rack accessories for bikes, skis, etc., however, most of the bike etc. accessories for Yakima and Thule racks can be used on either brand's bars or factory bars.
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