Someone once suggested restricting the magic items in Monsters & Treasure such that each entry on the random table represented a unique item. Thus, there is one plain Sword +1, one Sword +1, +2 vs. Lycanthropes, one Armor +1, and each of the miscellaneous magic items is unique. The exception would be potions and scrolls.
What would be the effect of taking this to the extreme, for swords? That is, there is only one +1 sword, period; if you don't roll the +1/+2 vs Lycanthropes, there isn't one. That means there are only five magic swords already in existence: +1, +2, +3, Life-Stealing, and Cursed. Any roll that duplicates a sword already found is replaced with a fancy mundane sword and either a potion or a scroll.
That doesn't mean that a wizard can't try to make a second +1 sword, but I'd consider making the enchantment process more interactive. That is, when the wizard finishes the +1 sword, roll for its abilities as if it were found in a treasure trove. If it has special or extraordinary powers, the wizard is told that the sword isn't finished for some reason, although it looks fine; a Contact Other Planes can be used to figure out what additional ingredients are necessary to activate the remaining powers and make the sword complete. The wizard won't know what those powers are.
To compensate for the existence of monsters that can only be hit by magic weapons, I would allow a Bless spell to be used on a weapon to make it temporarily equivalent to a +1 weapon, although without a bonus to hit.