Most of the waypoints I've encountered were dd mm.mmm but I've seen all other variants too. Including the various national grids - although I need to admit that was not in aviation.
Need to be careful inputting them, but you also need to be careful in selecting the right datum. WGS84 seems to be standard these days in aviation, but just two weeks ago I had a major gaffe with some Italian charts that were in some datum dating back to the 1950s. As it turns out, between WGS84 and that 1950s datum there was a half-mile difference. Not really significant when flying, but very significant when you're hauling 30kgs of luggage on your back (half of which was water).