Some that have yet to be mentioned
The Wanderer Guild line from Goodman and 3 AM- Monsters of the Endless Dark, Monsters of the Boundless Blue, Primeval Groves (all GG) and Monsters of the Savage Snow (3 AM).
The Template Troves trio from Silverthorne.
Beast Builder (no monsters, just advice) from XRP.
And speaking of which, Savage Species doesn't get a lot of love but does have some useful advice in creature design if you look at it right.
Behmoth3 had 2 interesting books based on one creature apiece- Maze of the Minotaur and A Swarm of Stirges. There are more creatures in each and Minotaur has one rather amazing idea on monster advancement.
The Creature Weekly series (which made 7 weeks and then 4-5 a year or two later) from Octavirate Games have all kinds of weird and interesting creatures. This is pdf only.
Ronin Art's Six Swarms and Throwing Dice Games' Notebook Essentials: Swarms, Stampedes and Skirmishes add a lot to the idea of the swarm subtype.
And finally there is Genjitsu's A Flock of Foes- creatures from the MM with templates already applied and 4 templates on making anything into the 4 basic golems. More interesting than it sounds, there is advice on how to make changes beyond what the template states.
And for the Deluxe Book of Templates, both 3.0 and 3.5 are worth owning. They cut somethings I consider significant in the 3.5 update (the worse being how to use templates section at the end).