Ah, bike racks. FWIW, here is what I think:

1. Raingutter mounted racks and their ilk:

Advantages: Will not damage the paint on your car or on your bikes. Very secure. Components are typically part of a system that allows you to use for skis, canoes ... all kinds of things, or to increase the package capacity of your car.

Disadvantages: Bikes are in the airstream and likely to get hit by bugs, and whatever else is going by at 70 MPH. Plays havoc with your vehicle's gasoline mileage. If you forget the bikes are up there (easy to do), you could destroy the bikes and/or do a lot of damage to your car. Leaving rack on car (even when not transporting bikes) also impacts gasoline mileage somewhat and can result in a lot more howling wind noise (can be reduced by a fairing, but that costs $). Can be difficult to lift bikes high enough to mount on rack, particularly if mounted on a van or an SUV.

2. Trailer hitch mounted racks:

Advantages: Unlikely to damage bikes or car. Holds bikes out of airstream, so gas mileage is less effected and bugs are less of a problem. Not too expensive if you're getting a trailer hitch anyway. Can be used for other things (skis, snowboards) but not others (canoes).

Disadvantages: Gotta get a trailer hitch ($ if you weren't otherwise interested in one). Some models make it difficult to enter tailgate or truck when attached. Depending on design, may cause problems when entering/leaving steep driveways ... not a problem with better designs.

3. Trunk mounted racks:

Advantages: Relatively inexpensive. Easily removed and attached.

Disadvantages: Will likely damage the paint on your car and/or your bikes ... the only issue is how much, and how long it takes. Typically do not allow access to trunk/rear hatch when attached.

What I do: Transport my bike by putting it in my car (wagon) whenever I can. The bikes are out of the airstream and so I get better gas mileage and the bikes bikes won't get rained on bugged up, or stolen. When I need a rack, I use the roof mounted variety as I have no other use for a trailer hitch, and I do use the rack for other sports equipment (skis, boards, canoe) and for other transport.

YMMV. :-)