As in, the highest rank or class. A football team might be referred to as top flight if they play in the highest league, for example.
I’m thinking it is related to the use of “flight” as a unit of the RAF. A flight is a smaller unit than a squadron. My wild arsed guess is that being in the “top flight” means you are in the best unit.
Another possibility is also from Wikipedia: http://en.wikipedia.org/wiki/Top_Flight_Handicap and another usage of “top flight” I have run across is a brand of golf balls.
I think it’s related to wine. A wine flight is a selection of different wines assembled for tasting purposes. A top flight is a selection of the best wines.
My impression is that it has little or nothing to do with “flight” meaning an instance of aviation, as in “I caught the 10:00 flight out of O’Hare” or “Some birds regularly make flights in excess of 600 miles.” Rather, it’s another usage of “flight” as synonymous to “floor” or “stor(e)y” – and a “top flight” object or substance would be one of high quality, suitable for penthouse or top-story luxury tastes.
I’d vote for this one so far! 
May also have foxhunting origins. The most skilled group of horsemen, those able to confidently clear any forseeable obstacle, follow the hounds closely and are known as the “First Flight.” Depending on the number of people participating, the field may be further subdivided by ability (“second flight” on down) with the lowest level group called “hilltoppers” because they go around any jumpable obstacles and watch the action from nearby hilltops without following closely.
“First flight”/Top Flight indicates the highest level of ability or quality.
It almost certainly came from “first flight” which is cited in British English from 1852 by the OED. The OED isn’t too clear on just where “first flight” comes from in useages about the top level of something.
“Top Flight” is American English, from everything I can find, and appears around the first decade of the twentieth century.