A feature of the human race is that they get an extra feat and extra skill points.
If a player decides to play human with a half-troll template (Fiend Folio p.93), does he still get his extra feat and skill points?
Because humans do not have a monster entry in Monster Manual, it is difficult to know if the bonus feat and skill points are “special qualities,” “specal abilities,” or whatever, however, the half-troll template is pretty straightforward:
The half-troll uses all the base creature’s statistics and special abilities except as noted here. [...]
Special Attacks: A half-troll retains all the special attacks of the base creature. [...]
Special Qualities: A half-troll has all the special qualities of the base creature, [...]
Since all of this is getting everything from the base creature, that means that the bonus feat and extra skill point features remain intact.
Now, half-troll does address skills and feats specifically. In both cases, it is merely reiterating that the half-troll template is not applying anything special here, though it could be clearer in the skills case.
Skills: A half-troll has skill points equal to (2 + its Int modifier, minimum 1) × (its Hit Dice + 3). Treat skills possessed by the base creature as class skills and other skills as cross-class. If the creature has a class, it gains skill points for class levels normally.
This is literally just the rules for handling creatures’ skills, as normal for a creature of the giant type, which the half-troll template gives to the creature. It could be clearer that this is just reminder text, but nonetheless it is just reminder text. Ultimately, though, since “it gains skill points for class levels normally,” and a half-troll human has only class levels (no racial hit dice), it doesn’t end up mattering because we know the creature handles skill points “normally.” Since nothing changed the extra skill points feature, “normal” for a human includes those extra points.
Feats: Half-trolls gain feats normally. [...]
And this is the same deal as skills were: the half-troll is gaining feats normally, and normal for a human, or anyone else with the human bonus feat feature—which the half-troll still has—includes an extra feat.
Pretty much every template ever uses this same wording, saying that the templated creature gets everything the base creature had plus some additional stuff. There are some exceptions—dragonborn from Races of the Dragon immediately springs to mind—but they are rare. In fact, they are so rare that cases like the dragonborn explicitly spell it out—which means if you did find a template that neglected to handle it explicitly, you should assume that the author simply assumed that retaining the base creature’s features was the default, and forgot to use the usual text.