Rayquaza (Only if you obtain both Kyorge and groudon; groudon is exclusive to soul silver)
Dialga, Palkia, Giratina ( Only with the event Arceus)
Latios, and latias (Only with the enigma stone wifi event)
The amount of times to rebattle these Pokemon is unlimited as long as the elite 4 and champion are beaten after they faint. Upon capture they will not appear for battle.