Here's the latest version of what I use, based heavily on Crothian's system. Feedback is appreciated.
Every weapon falls into one of 8 categories: Slashing (swords), Chopping (axes, polearms), Piercing (daggers and spears), Blunt (maces), Thrown, Projectile, Natural (unarmed, gauntlets, natural weapons), and Ray (ray spells and firearm-like weapons).
Each category is then divided into three groups: Light, Medium, and Heavy, based on the size of the weapon relative to the user. Note that Natural and Ray only have Light groups, so there are 20 groups total.
All people are proficient with all Light weapons (8 groups), regardless of category, except that Exotic weapons have special rules. Most of the existing simple weapons fell into the Light category anyway.
For heavier weapons, you choose specific categories as you go along.
All weapon-using classes (anyone that gets anything beyond simple weapons in the core rules) gets one free category of their choice at Character (not class) Level 1. It's like the max HP die and 4x skill points you get at level 1, it's a bonus for starting as that class.
Most weapon-using classes get one specific category at Class Level 1; Rogues get Piercing, Barbarians get Chopping, Paladins get Blunt, Monks get Thrown, Rangers get Projectile, Psychic Warriors get Slashing, and Fighters get (Any 1). So, if you have a Wizard and multiclass into a Rogue you now can use piercing weapons like the rapier, but it's not as good as if you had started as a Rogue.
Then, each class gets an additional category every few Class Levels. Fighters get them at levels 3, 5, 7, and 9; Rangers/Paladins/Barbarians/Psywarriors get them at 5, 10, 15; Rogues and Bards at 6, 12, 18.
One of the things I hated was how people would take 1 level of Ranger, let's say, and suddenly gain knowledge of all weapons.
Martial Weapon Proficiency feat gives you a category, no matter what size the weapon is, so you can only take the Feat 6 times at most.
Weapon Focus, Weapon Specialization, Improved Critical, etc. apply to all weapons within a given Group (Medium Slashing for example). So, training with a Longsword doesn't help you with a Greatsword, but it would help with a Scimitar.
Anyway, that's the basics, I really reworked the Exotic Weapons; each has a "normal" group, and an "exotic" group like Heavy Weapon (Bastard Sword, Dwarven Waraxe, etc.) that gives you extra benefits if you take the EWP in that group. A few have multiple exotic groups, like the Katana.
