Beer with a nice nose (hoppy or malty aroma) is better from a glass, especially one with a wide mouth. The head on some beers can actually improve the flavor and mouthfeel. Anyone here ever tried Guiness?

Some beer is prettier than others. Something with a nice or interesting color can be better appreciated in a glass. A nice Bavarian Hefe-Weizen fits this description pretty nicely.

Yum.

Bottles have the advantages stated above. They're convenient, easy to carry around, and involve less clean-up. You typically drink more slowly from a bottle; you can decide whether this is an advantage. Also, your beer comes with a nice blue-collar image at no extra charge! Any beer CAN be drunk from the bottle. The less aromatic or pretty a beer is, the less reason to put it in a glass. Your typical "American light lager" doesn't suffer from being pulled straight from the longneck, IMO.