I believe (not positive) that most teams charter planes that are in regular service with the airline. Ofcourse that may not be the case for teams with dedicated planes during the season with the livery advertising the occupants. Most NBA teams fall in that category.
I've heard stories from the 49er Travel Manager getting a coniption because United didn't have their aircraft waiting for them (tough nukies, they shouldn't have top priority). However, that implies that the plane was used while the 49ers were in New Orleans.
The Raiders were using a Hawaiian MD11 (at least going to New England for the championship game). I don't believe that was a specially equipt plane for them either.