Swarms, incorporeal creatures, and certain kinds of regeneration can all completely shut down an unprepared party, with little chance of a workaround.
Of course, depending on how the regeneration is canceled you can obtain counters at early levels if you're thinking ahead and are willing to shell out the gold. Swarms can be similar, depending on where you fall on the whole "splash weapons against swarms" debate.
Still, they can both technically still serve that sort of "gateway" function, even if its a gateway you can go through fairly early (so long as you're experienced enough to know how important it is to prepare for).
Depending upon the circumstances, suffocation (drowning, burial, choking, hanging, etc.) might work against regeneration, depending on terrain. Once the enemy is down, you can just keep on hitting it until you can find a way to make it suffocate.