In addition to what StasM pointed out, photon torpedoes had many uses. They were notably used as caskets and flares, by stripping them down to empty "torpedo casings". As far as what makes them preferable to more conventional warheads, photon torpedoes were known for their extremely crippling and damaging explosive yields. In fact, if a photon torpedo was fired at a target in close range, the explosion could end up disabling the firing ship in addition to obliterating the target.
Photon torpedoes weren't only ship-to-ship weapons, but served ship-to-ground roles as well. The torpedo's shielding can allow it to bury itself into a planet's surface completely intact. They were highly effective for destroying ground-based targets from inside itself. A 25 isoton torpedo could destroy an entire city in mere seconds.
Another great thing about photon torpedoes was they could be modified to different explosive yields and firepower. So you could fine-tune a specialized torpedo for a specific task on-ship. Essentially, the photon torpedo became the goto weapon when the Federation wanted to proverbially "get shit done." (Pardon my terminology.) These babies gave you a lot of bang for your buck.
Source: Photon torpedo on Memory Alpha