A crossover is where aspects of two or more distinct fictional universes are included within the same story.
Star Trek universe
Episode 3, "Cybernetic Heartbeat", of Star Trek: Brave New Worlds involved a crossover with Star Trek: Pretoria. Both series were separate message board forum role playing games on the now defunct The Helix BBS in 2004. Each RPG runner, Hawku (at the time known as Aku) and Birds of Prey, merged each series' next "episode" to start as one thread where RPG player/writers from both series would write their character's experiences in a shared situation.
With other franchises
Some early episodes of Star Trek: Phoenix-X crossed over with other fictions. "Fight, Parts I, II & III" crossed over with Xena: Warrior Princess. "Alien Interference" had a subtle crossover of the Alien (Alien franchise) into the Trek universe.