Well, a couple of NBA 2Ks ago, I recall the 2001-2002 Sacramento Kings being a classic team that you'd get as a code for preordering the game (I think that was for 2K13 -- correct me if I'm wrong).
The 2000-2001 Philadelphia 76ers have been in the game for a couple of years, too. (Of course, Allen Iverson is pretty well beloved in the lore of basketball gaming, and that team made the Finals that year.)
Trying to think of other examples. Can't remember if 2K15 had them, but I know a few years ago one of the early to mid '90s Denver Nuggets teams (Dikembe Mutombo) were on the game.
I bet a lot of people will use that '99-'00 Raps teams purely for Vince Carter dunks. For T-Mac I'd rather see the '02-'03 Magic or '04-'05 Rockets (with Yao). I'm a sucker for classic teams, even if some of these aren't really all that old.