I tend to prefer draft beer, so I'll go with glass/mug.
I like draft beer too but I mainly drink at restaurants and many of them don't clean their beer lines on a regular basis. So I go for bottles a lot.
That is a fantastic point, and one a lot of people don't realize. Drink draft beers from local brewers, esp those with independent distributorships. There is a much higher chance that they're sending a guy around to do that every week or so.
EDIT: I have a good friend who was a CSR or whatever (the guy who sells beer and taplines to bars) for Harpoon. He gave me this tip, and if the rest of the brewery busts their butt as much as he does, if you're in Boston drink Harpoon.