Here are a few more ideas on possible sources for monsters:
Offensive terraforming. The ancients were actually invaders from another planet or plane. They seeded the setting with monsters that came from their homeworld, most with specific functions in mind. Some were meant to exterminate and replace the natives, others to perform labor (this is where humanoids such as orcs come from) and the rest to fill out the ecosystem. A variant is having the monsters created to act as raw materials- the aliens want to use their parts in magic, alchemy or even technology and are willing to replace entire planetary populations to do so. For the most powerful form of terraforming, it may alter the reality of the world as well. This means the planar traits (or magic signatures if you have the Morningstar setting) are changed as the monster populations are introduced. Reversing this may seem like a good idea but it probably will cause as much chaos as the initial change did.
Nightmares come to life. There is an early d20 setting that did this, Hunt: Rise of Evil, and even though I didn’t care for the nations, I did find the two monster books fascinating. That world is populated by dreams and nightmares of Earth. Most monsters in D&D (and spin offs) are nightmares so why not just use that idea as is? People within the setting dream of terrible things and something brings them to life. This can be very different from other settings in that there are no species of monsters that breed. Everything is created as unique creatures and the very nature of people means that there will never be a shortage of monsters to prey on them.
Cursed people. How I read the Masque of the Red Death setting is that all intelligent monsters are people who cursed themselves by their deeds of evil. Ravenloft, the parent setting for MotRD, has rules for corruption, turning people into horrors but it shouldn’t be difficult for you to come up with your own ideas on how this might work. Unlike nightmares, these creatures do breed and may even evolve in the flesh and/or behavior. Werecritters and other shapeshifters, where some of the original person remains may be the most common form of this source, but I don’t see any reason to exclude anything, from oozes and zygoms to demons and beholders.
Spontaneous generation is something I have been playing around with for a few years. The idea that life comes from lifeless material works well enough as a source for many monsters but I prefer a combination of living and non-living sources. For example, a colonist of a new world/plane plants some acorns. After the trees mature, squirrels, turkey and deer appear even if they were not introduced. These animals come from the soil or water in or near the new forest and act as if they were there forever. The advantage of this source is that once a monster’s origin is identified, it can be altered or neutralized. Another variant of this is a spirit that causes new life to appear. A stag or hart could cause whole forests to appear in the middle of deserts or on dead moons.
