Here's a system my current DM came up with, which has been great fun:
First, some assumptions I hold. The first is that the PCs and the Enemies are the interesting parties in this conflict, not the hodge-podge of friendly NPCs, cohorts or minions. We don't go into combats to hang around and let the DM roll dice against himself.
Secondly, battles in D20 are slow and complicated enough as it is, and we want to inject as much flavor and fun into them as possible, not just slug it out to inflict maximum damage as quickly as possible.
With this in mind, our DM opted, in a rather large battle with a pack of mutated bulettes where we were helped by about 15 soldiers and scholars, not to have those NPCs actually have their own initiative scores and attack rolls - this was our fight, and we didn't want to take the narrative focus off of that. What he did do was allow us to use them as helpers for any actions we want to take. If it was cool, they added bonuses.
For example, one character might shout out to the soldiers to fire their crossbows at the bulette. He rolled a Diplomacy check, had a good roll, and the DM ruled that their half-hearted bolts, while not harming the bulette directly, distracted him enough to offer the character flanking while he attacked. Another character might use them for cover. And at the battle's climax, another character called up all the NPCs together, along with a casting of Create Water to turn the ground to mud, to serve as assistants in a massive Bull Rush maneuver to push the giant bulette into the lake.
This served several purposes. The first, of course, is to minimize the time spent doing actual combat for boring NPCs. But importantly, it allowed the players to let their creativity run loose, and do bigger and cooler stuff than we would do normally in combat.