Going by the examples in the core rules, I usually assume the following in my games:
* Humans can interbreed with elves and orcs, producing the standard PH hybrids. The reason why they can are a bit murky, and may involve common ancestors and/or magic in the creation of one or more of those races. The only other standard races that can interbreed are half-elves with elves and humans.
* BTW, I still use AD&D 2E's simple rule for determining the race of a human-elf hybrid: If 50% or more of the character's ancestors were elves, they were a half-elf; if fewer than 50%, human.
* Dragons capable of polymorphing can produce half-dragons, per MM.
* Many outsiders can interbreed with Material Plane races, resulting in half-celestial and half-fiend hybrids. At least among human-outsider hybrids, once the outsider blood is diluted further, you end up with planetouched.
* A number of MM monsters (such as owlbears) must be the result of magical experimentation. In one of my campaigns, I created a wizard villain who did such work, and created a new spell, accommodation, to enable it.
Depending on the game, I then borrow some or all of the following from other sources:
* Some elementals, and outsiders with an elemental subtype, can interbreed with Material Plane creatures, creating half-elementals (Manual of the Planes). Once that extraplanar bloodline is diluted, you get genasi (Monsters of Faerun).
* Green Ronin's Advanced Player's Manual has a template for adapting any material creature to become an aligned or elemental planetouched, which allows for much more diversity than standard planetouched or genasi. (That book also has rules for building new races, including new hybrids of PH races, but I've yet to try them out.)
* GR has also published Aasimar & Tiefling (new halfbreed races, some of them extremely exotic) and the Advanced Bestiary (new templates of all kinds). I only own the latter, which contains a few hybrids (half-drow and half-giant, for example) plus the ultimate hybrid generator, the Amalgam (combine any two monsters to create a new one). The latter is easily the most complicated template in the book, but if you want to go there, it's exactly what you need.
*Stormwrack includes some new subraces, such as the aquatic half-elf.
In my games, I rarely use all the demihuman subraces from the MM--deep dwarves are simply PH dwarves, I only use the standard PH halfling, and I often ignore gray elves and forest gnomes.
I normally limit my players to races with no Level Adjustment, or +1 at most. This rules out half-celestials, -fiends, and -elementals, though NPCs of those hybrids exist. (The whole concept of LA tends to give most of my players headaches anyway.)
In the campaign I'll be starting soon, I'm being more generous than usual about the range of races I'm allowing. For example, I'm allowing aquatic half-elves and the APM's planetouched template (LA +0 for elemental, LA +1 for aligned; one PC will be a water PT human). But I'm still barring races that are hard to explain even in the melting pot of GR's Freeport setting.