I handle this basically the same way 4E does: for critters that aren't that far out there, I create a custom comparable-to-human "player race" that has reasonable stat bonuses and a feasible "signature ability" associated with the critter.
For example, minotaurs would get +2 Str, +2 Con, -2 Int, -2 Cha, the Powerful Charge/Gore, immunity to mazes, and be described as "huge and hulking" even if they don't get reach or the mechanical modifiers for large size. Or, if the player absolutely couldn't live without being large size, treat them as being +1 ECL and charge them an "Exotic Background" feat.
If at any point the player were to kibitz about "normal" minotaurs having more abilities (never flat-footed, skill bonuses, etc.), my reaction would be, "When you are a CR 4 critter, you'll have all sorts of abilities they don't -- like weapon proficiencies and a bucket of feats. Get over it." Because I've found that when presented with the idea of actually playing a 1st level "monster class," most players balk at not having any class abilities, skills, or armor proficiency to speak of.
However, at some point, I just say no. I've never actually had a player want to play an adult dragon, so it hasn't been an issue. But I do have one who's constantly wanting to play gnolls (+2 Str, +2 Con, -2 Int, -2 Cha, Darkvision, +1 natural armor).
-The Gneech
