It would help to have a better definition of what you mean by a point-buy/skill-based system. HERO is point-buy but is not really a skill-based system, as it is based mainly on powers. D&D 4th Edition could be called a point buy/skill-based system as it has point buy stats and skills. I'll assume you mean skill-based as opposed to class and level-based.
As others have pointed out, the main benefit of skill-based systems is that the players have fine control over character advancement. Also, it allows characters to be incompetent in some areas, as things are not as inter-linked as in a class-based system.
The biggest problem is that they are hard to balance, as it is easy for characters to focus on certain areas, and if the area that one character is focused on comes up all the time while another character's focus seldom does, then that can lead to dissatisfaction.
Here are some other game systems that might fit what you're looking for: Runequest II (from Mongoose) has options for random or point-buy character generation, and pretty much everything is based on skill rolls, it uses the Basic Roleplaying (BRP) system, a free BRP quick-start is available online;
Ars Magica has a focus on magic and spellcasters, including a detailed magical research system, however it has some quirks to the gameplay;
White Wolf's World of Darkness system is largely skill-based, see Mage the Sorceror's Crusade for the fantasy version;
Mutants & Masterminds is a d20 based superhero game with a point buy system, there is a Warriors&Warlocks supplement for fantasy games using the system;
FATE system is largely skill-based, and the SRD is free online, see Legends of Anglerre for the fantasy version and fantasy specific rules;
D6 System is largely skill-based and the books are available for free on rpgnow.com;
Reign uses the One Roll Engine, and rules for mercenary companies and micro-and macro-level deeds interacting;
Burning Wheel is skill-based, but can be very complicated, a simpler version of the system is Mouse Guard, which can be used to run ordinary fantasy games.