In one of the Dragon Mags waaay back in 2e, this was presented as a Kit, a way for a mage to create stuff like Girffons and Owlbears, as well as to alter creatures aswell.
There were spells that allowed you to combine critters, in a magical ritual, as well as add things to them (wings, tentacles, etc), bestow a spell ability into them atleast 4th level (Like giving a wolf the ability to breathe lightning, or a lizard with a Hypnotic Gaze). As well as do things like up their intelligence.
I created an NPC in my campaign world that's basicly the head of a Conglomerant (He has three outlets in the world) that do this: They create mounts, guardians, and pets for anyone who orders it. His guardian was a Bipedial Winter Wolf, and he actually hired my party to go bring two live, breedable winter wolves from the north for experimental purposes, making more like his bodyguards, or atleast, have more potential test subjects.
The party actually ran aground one of his creations; a Darkmantle that bred through spells and several generations to look like a Chandeliar.
Anyways...
I would say the Tauric Template in the MMII is one way to go. Also start considering some spells that would allow this (But I would think they would require some hefty components, Fine specimens of the species, and some serious time).
I would also suggest perhaps tooling spells like the kit. Or, even better, a Prestige Class.
Possible things that I can suggest: A Prowl (A dire panther or panther combined with a giant owl), perfect for night operations. The same can be done with a Cougar/hawk. Combing amphebious creatures with predators, or those creatures with various modes of travel (Fly, Burrow, Swim, etc etc), and those with unique abilities. Also varying sizes for creatures; a behir the size of a german shepard, for instance.
I could come up with some game mechanics if you like?
