Bunks all the way.
1) The trailer is lower to the ground. This helps when towing in the wind (Columbia Gorge). It makes it easier to get in and out of the boat when it is on the trailer. This is more important the bigger the boat and the higher the gunwales. It makes it easier to get the boat into a garage if you are so blessed to have room in your garage, as the over-all height is lower.
2) It is easier to get the boat up on the trailer. Under speed it slides right up to the top. You actually have to be a little careful so you don't crash into the upright. In the wind it can make the difference between 1 or 2 tries and 6 or 7 tries.
3) I think the hull is better supported. Think about hitting a pothole at 30+ miles an hour and I prefer the force being spread out along the entire hull and not just many quarter-sized points. It can save a cracked glass hull and weld strains in metal boats.
4) Easier and cheaper to maintain. You can get replacement bunks and carpet at Home Depot and have it all replaced in about 2 hours. Finding/ordering rollers and then trying to get the bolts un-done can cause elevated stress hormones.

5) Not so important, but nice just the same is the fact that I have never seen anybody launch their boat ON the ramp that had bunks. That task has been left to roller trailers in all the cases I have witnessed.