After quests have been completed, or during the course of completing them, my Player Characters might pick up new armor or weapons that I've put placeholders in for, but eventually I reach a point where I need to create stats for these custom weapons or armor (that are not based on equipment in the various published books). What is the best way to manage how much damage these weapons inflict, or how much extra protection the armor gives the player?
In terms of enhancement bonus, players should start finding +1 gear almost immediately, +2 gear around level 5, +3 gear around level 10, +4 gear around level 15, +5 gear around level 20, and +6 gear around level 25. Note that any armor that has a high enough enhancement bonus to be masterwork should always be the best kind of masterwork allowed for its enhancement bonus. Masterwork armor is a math fix for the way player defenses tend to lag compared to monster attacks as party level increases; it is not something special that players should have to work to get.
In terms of special abilities, weapons that give a conditional bonus to damage (against enemies of a specific type, against enemies larger than you, on your attacks with a specific keyword, etc) usually give an item bonus equal to their enhancement bonus; weapons with an unconditional damage bonus are very powerful.
Armor and neck items that directly give extra protection are unusual and rather powerful; most give a daily item power, a skill bonus equal to the item's enhancement bonus, or both. If they do give a protective boost, the most common is a +2 bonus to 1 or 2 defenses when a common condition is met (you shifted this turn, you're a druid in beast form, etc) or against certain kinds of attacks (close attacks, ranged attacks from 5+ squares away, etc).
Remember: damage bonuses should go up as the party gains levels, defense & attack bonuses should not (except for enhancement bonuses).
A good item gives one, maybe two of: a very small always-on bonus, a moderate conditional bonus to damage/attack/defense, a moderate always-on boost to initiative or 2 skills, a daily power equivalent to an encounter utility power or capable of making an encounter power closer to a daily power in strength, or an encounter power equivalent to an at-will utility power.
If you want an more powerful item and/or an item with lots of roleplay significance, take a look at artifacts (which unfortunately are spread around in a variety of books) for some examples and ideas.
If you have DDI, an easy way to estimate how good items should be is to look through the compendium and see what magical enchantments already exist for that item at that level.
The easy way is to pick out items that are already present in the Player's Handbooks and Adventurer's Vaults, etc. and make slight modifications—adapt, modify, and merge as you see fit. There are many options out there, saving you a lot of work.
The easiest way is for the players to do it and submit their items for approval by you and the rest of the group. This saves you all the work.