Skills run the gamut from extremly useful (Concentration) or even "required" (Search) to useless (most Knowledge skills).
The game rules do not make it easy to use "less useful" skills. These skills require description to be useful, and if neither the GM nor the player know anything about the skill in-game, then it becomes "roll dice".
For instance, I was reading a few weeks ago a book about near-future space exploration. (Exploration is probably not the right word - they didn't even go to Mars. Whatever.) In one scene, a pilot rescues a stranded astronaut. The text went into some detail about the physics of the scene - the pilot was spinning too fast, so it was dangerous (for reasons I don't exactly remember, as I'm not a space phycisist), and he ran the risk of accidentally killing the astronaut while he was at it. As it was, he rescued the astronaut (successful skill check) but damaged some part of his spacecraft.
You'll never see such description if neither the player nor GM know nothing about flying a spaceship (and, most likely, they won't). Furthermore, if the player knows more about the subject than the GM (there's more players, so this happens often) it causes conflicts. Finally, that bit about the unintended damage... where's that in the rules? If the GM said something about that, the player might complain. (Is that a player/DM problem?)
I've tried to mitigate this by using "complex skill" charts. An example would be diabling a mechanical trap. The trap has three parts, and you must disable all three pieces. If you fail by 10 or more on one check, or fail three times in a row, then the whole trap goes off. Give each a cool description. This only works if you're not putting lots of traps in your dungeon, if you know something about making traps (or at least saw a lot on TV, or have a real good imagination so you know what to do with a magical trap), if you expect the skill check (suppose your players all of a sudden invaded a castle which you hadn't drawn up and didn't have specified traps for it?) and, of course, only one player is making the check.
Skills that require opposed checks are used "all-or-nothing", IME. You either have a high Spot score, or you don't bother putting ranks in it. (This is very important to classes that don't have Spot as a class skill.) Again, description comes into play. If someone narrowly missed a Spot check, should they see something (but still suffer suprise)? If they barely made the check, should they see who is following them, or just know someone is following them?
Diplomacy, as written, is next to impossible to use, as it targets a fixed DC but is much more powerful than, say, Search or Disable Device. I'm disappointed in the effort that went into making that skill. I think Dragonlance tried to make the skill useful, but so far, I've only found Rich Burlew's houserules to be useable.
Some skills are difficult to use, the way they are written, at least for some GMs. I find using encounter distance rules and general Hide/Spot to not be easy to use. As a result, surprise rounds come up less often than they should IMC (screwing over anyone with lots of ranks in stealth or awareness skills).