The main concern is choosing a song (or portion of a song) that is too short, meaning that there would be an awkward silence somewhere during the service. You'd hate to be in the middle of a long aisle when the song stops playing! You'd also hate for there to be an awkward silence as the bridal party is walking down and before the bride enters.
If you are choosing to use recorded music (iPod, CDs, etc.), I would err on the side of songs that are too long than too short. Have the person in charge of the iPod or sound board start fading out when he/she sees that things are coming to an end. This is much better than stopping the music abruptly, and you won't have to time things exactly at the rehearsal, which makes things a lot less hectic. I would pick a song that's at least 2.5 minutes long for the bridal party, and at least 1.5 minutes long for the bridal processional (depending on the size of the space).
Better yet, hire a live musician who can watch as the ceremony is happening. An experience wedding musician can extend selections when needed, and can come to a nice close when you've reached the altar or ceremony space.
Hope this helps!