Try this. Watch a college football game, preferably a conference game, with fans of either team. At some point, a referee will make either a mistake (because he is a person) or a fair call that upsets your viewing party (because they are people).
At that point, you'll hear something like this: "Typical [conference name] refs." Everyone will agree that [conference name] refs are always this bad. If you don't always watch this conference, you'll try to speak up for the badness of your conference's refs, but no one will have any of it. They'll start citing the [year] [school]-[school] game in unison, as if you watched it.
While we have no way of knowing which conferences miss the most calls, we do know which conference's refs blow their whistles the most.
The numbers from the last five years for each league:
Also, every team in the country ordered by how many penalties it racks up in conference games, based on the last five years:
Most interesting, perhaps, is the team's that switch conferences, with easy narratives sitting right there for Boise State and Texas A&M especially. Over the last five years, teams on their way out averaged 5.758 flags in conference games, while new guys averaged 6.217. Hazing!
Also worth noting Oregon, one of the most successful teams of the last five years, tops all BCS programs, with Rose Bowl victim Wisconsin drawing the fewest conference flags. It's like penalties don't really matter all that much!