One of those things I remember fondly from my early days of playing D&D was that PCs would sometimes end up using strange weapons (often tridents, for some reason) because they’d find some really good magical ones. Making (or commissioning) your own magical weapons to spec was prohibitively expensive, and most GMs I played with (including myself) didn’t make magic weapons readily available in stores. Couple that with the fact that early versions of the game had an absolute version of damage resistance based upon the “+” of the weapon (e.g., +3 or better magic weapon required to hit), and you had good reason for PCs to stick with the most powerfully enchanted weapon they could find.
In many fantasy novels (and other source material), a hero’s weapon may not be magical, but it is often not interchangeable with any other weapon. A character might be particularly skilled at using a given weapon… and weapons are often ascribed with legendary importance due to tasks that have been undertaken with them.
How to capture some of this in d20:
In D&D 3.5 it is more-or-less expected that your primary magic weapon will have a +1 equivalent for every four levels or so.
Each time your character gains a level, you may assign one of her weapons as favored. This must be a weapon that she has used. After every second consecutive level that the same weapon is named favored, she may add a +1 competence bonus to either her attack or damage rolls with that weapon. These competence bonuses stack with themselves, but not with other competence bonuses. Each time the weapon is enchanted after it has been named a favored weapon, the PC must get used to the new ‘feel’ of the weapon. For every +1-equivalency that a weapon is enchanted with, the PC loses a +1 competency bonus to either attack or damage (player’s choice).
The expected upshot: PCs will stick with magic weapons they acquire early in their careers. Provided they have access to someone who can further enhance them, these weapons may end up being marginally more powerful in their hands than other weapons of similar magic.