"Actually takes time and skill to beat..."
If you want skill, Demon's Souls is the top contender of any recent games (like within the past 5 years.) It's really challenging, though characterization is non-existent. It also takes a good amount of time and keeps up the challenge throughout. It's very different from pretty much everything else.
Persona 4 is excellent and fairly challenging, and about a 80 hour game if my save file time can be trusted. Its sheer amount of content is breathtaking. Persona 3 also applies here, but 4's slightly better in a number of ways.
Final Fantasy Tactics is tough and very tactically minded, unlike the majority of RPGs. A good story too, though you'll probably miss most of it on a first playthrough.
Baldur's Gate 1 and 2 are significant contenders here. They're pretty tough and allow you a great amount of tactical leeway.
The Disgaea series is interesting and takes a very, very long time to complete; the combat isn't as deep as the previous entries however.
Planescape: Torment is awesome, but the combat's (and therefore the challenge) is lacking. Arcanum has the same problem, but I'd still recommend them for the excellence of their settings (and other parts).
If you can stomach the ASCII or simple graphics, a very evil random number generator, and permanently losing your character when you die, you will find Nethack a challenging, time-consuming game that is utterly insane in its attention to detail and very replayable. No actual characterization to speak of, however.
I personally wouldn't call KotoR 1/2, or Bioware's games before Dragon Age or Bethesda's games as needing much skill to beat, actually. Just to comment on some of the suggestions offered.