Lets see, had more monsters, Also the source code is available on that site.
() had well made dragons (several types) and a few boring reskins of stock monsters with increased health etc.
had Fiendlings and some kind of wizard. Most of Kona's maps seem to have some custom enemies so its worth checking all those maps.
had re-done Nehahra barons.
Some other mod from Tronyn (can't remember the name) had axemen, some reskins (not as boring, they had different attacks etc), and the wizard dude again. EDIT: the name of this series is .
had a few new monsters.
There was this big moon base map? Had the walking mechs that fired lasers from Custents. EDIT: the name of this map is .
has enforcers with rockets flame throwers.
There is yet another Base series with a flying laser drones and a new reskinned set of blue enemies that have different attacks. EDIT: the name of this series is .
Hexen 2 is based on the quake engine and had a shitload of new monsters. I you somehow managed to find/rip the qc source code I'm sure it could be made to work in Quake.
Prydon Gate
AirQuake/KiU/DiD tanks and stuff
And not to forget my own contribution, the maggot and the stalker. Don't know what happened to them though
BTW, if you are intending to have _every_ monster in your zoo map, you'd better have a custom engine that can handle oversize progs.dat and increased precache limits. One of my n00b mods tried the same and hit the limits way before getting all the ones listed above.