Short term reasons.
Brake inoperative or removed, gear stays down for 2 minutes to allow the wheels to spin down.
Nose wheel buffer missing, gear stays down for 2 minutes to allow the wheels to spin down.
Longer term reasons.
Brake cooling, especially is you are taking off from a hot airport on a short flight.
MEL item requiring a gear down flight (We are not allowed to do this with pax)
Can anyone think of anymore?
Mutt.
(Needless to say, these may not apply to all aircraft types)