Of the ones generally available at most places, I prefer strawberry milkshakes if they're done well. Some places don't do it well though. Chocolate is a good backup alternative though.
That said, some restaurants have special varieties available at different times of the year. Arby's, for example, has a really nice orange cream milkshake during the Summer months. I also like pumpkin spice/pumpkin pie milkshakes when some places have them in the Autumn months, but they're not that common, at least around here.