A mob is treated as a single creature in both 3.5 rules and PF rules so channel energy would simply target the entire mob as 1 creature and do +50% damage.
Also I think the PF Game Mastery Guide has mob rules.
I second Anvil's notion.
If that doesn't make sense to you, consider a rat swarm. A rat swarm has lots of hit points; it takes more than a single burning hands to destroy them all. But a single rat has one hit point. A single rat should die anytime it's hit by a burning hands, and a group of single rats should die when they're hit by a burning hands. Yet by becoming a rat swarm, they're able to survive it.
My point is -- running a mob of zombies in that way is consistent with the way that 3.5 and Pathfinder runs normal swarms. For whatever reason, there are defensive benefits to grouping up like this.
This would even be kind of consistent with how turn undead used to work -- if there were too many undead, it often wouldn't have full effect on all of them. So maybe your zombies are 'splitting the bill' on all this damage.
You can't really use the Swarm subtype for zombies.
Swarm Subtype: A swarm is a collection of Fine, Diminutive, or Tiny creatures that acts as a single creature...
...so RAW you can't have a swarm of Medium-sized creatures like zombies.
The way I've simulated huge masses of zombies who "swarm" over PCs is to create a new zombie type, the "mob zombie" that has the following extra special ability:
*Mob (Ex)*: A mob zombie has a reach of 10 feet through a square occupied by another mob zombie.
I also give them Improved Grapple, for a +1 CR value.
Zo, if the PC (represented by an "X") is totally surrounded by mob zombies, like so...
Z Z Z Z Z
Z Z Z Z Z
Z Z X Z Z
Z Z Z Z Z
Z Z Z Z Z
All 24 zombies can attack him... AND they all have a flanking bonus!
He already said he's using 3.5 rules for mobs, and those rules override the general Swarm requirement. I'll even point out that Pathfinder does something similar, given that in urban environments you can treat crowds of people like difficult terrain (which certain characters like the Lion Blades and Urban Barbarian can ignore).
Further, they seem like appropriate rules to use even with the switch-over of rules systems. The abilities of the creature itself certainly aren't out of line with Pathfinder design philosophy. Swarms are already a 'creature' made up of lots of creatures; Kingmaker's warfare rules do this too with armies. And his complaint of how damage would affect mobs already applies to swarms, so the disadvantage he brings up isn't something new or something we haven't already accepted and learned to justify or ignore.
Meanwhile, running 24 different creatures in a combat is 1) extremely tedious; 2) if they are following CR guidelines they are very likely to all die in one area effect attack anyway; and 3) there is a high likelihood that they are only going to be hitting PCs with 20s most of the time.
If I were absolutely bent on running a lot of zombies but didn't want to mob rules, I'd probably homebrew a smaller number of more-powerful zombies that could make use of Gang Up, Grab, Lunge, and/or the Morlock ability to occupy the same square.
You can't really use the Swarm subtype for zombies.
Swarm Subtype: A swarm is a collection of Fine, Diminutive, or Tiny creatures that acts as a single creature......so RAW you can't have a swarm of Medium-sized creatures like zombies.
The way I've simulated huge masses of zombies who "swarm" over PCs is to create a new zombie type, the "mob zombie" that has the following extra special ability:
*Mob (Ex)*: A mob zombie has a reach of 10 feet through a square occupied by another mob zombie.
I also give them Improved Grapple, for a +1 CR value.
Zo, if the PC (represented by an "X") is totally surrounded by mob zombies, like so...
Z Z Z Z Z
Z Z Z Z Z
Z Z X Z Z
Z Z Z Z Z
Z Z Z Z ZAll 24 zombies can attack him... AND they all have a flanking bonus!
But there are actually rules for a 'Mob' that he's using from 3.5. It's similar to a swarm, just for bigger creatures with a few extra abilities. It works just fine with Pathfinder. It actually was made to eliminate the headache of having to do things like roll 24 seperate attacks and calculate multiple cover for creatures in the middle of the mobe etc etc.
I would try looking those rules up because your scenario seems like a nightmare to GM. I think it would slow combat to a crawl. Do yourself a favor, check out the Mob template that can be added to any creatures from Dungeon Masters Guide II.