I always preferred skill-based systems, based on a strong dislike for the rigid nature of most class-based systems.

However, I must say that the way D&D 3-3.5 handles it has resulted in the most entertaining system I'm aware of that's been used in computer games.

That said, I think the SPECIAL system is pretty close and it's a shame they messed it up in Fallout 3. Probably the best skill-based system out there.