Trunk or Hitch Rack: Bikes stay a little cleaner, cheaper, easy access to bikes, access to trunk limited. If you are camping, and you can't get to the trunk without removing the bikes, it's a deal-killer. We drove across the country, and at every campsite we had to remove the bikes.
Roof: Bikes destroyed if you drive into your garage, bikes get dirtier, gas mileage affected.
Once we were meeting our daughter at the Vega airport. I anticipated that clearance would be a problem, but approaching the airport, there was a big "Clearance 7 feet" "warning" sign, but the sign itself went across the road, and was a big iron beam. IOW, the sign itself was a problem. My wife had to go back along the highway, and flag motorists over so I could back up, then zip across several lanes to avoid it. It was a mess, and I am always uncomfortable with the bikes on the roof.
Not my bikes:
