Meh. good points raised above, but I look at it this way. The purpose of gear in a raid is twofold - to reward players and to make the raid as a group more powerful. Thus, what you want to do is to be fair to the players who are contributing by showing up regularly but you also want to make sure that the gear is distributed in such a way as to help the raid overall. For this reason it's usually a bad idea to let people gear out a toon then sit it and bring in another toon. You've just sat a bunch of gear power.
I've always used one of two loot systems and they've worked fine both to make sure you're gearing the raid and being fair.
System 1: For static groups with high attendance (so 10-12 people for a 10 man, 25-27 people in a 25 man), roll, MS before OS. If someone's won something that night they get last priority on items for the rest of that run if another item for them drops AND if someone else in the raid can use it. The latter rule makes sure that one person can't get super lucky and win all of the items if there are others in the raid who can use them. Obviously this isn't an issue if only one person in the raid can use an item.
System 2: For groups with more people rotating in and out, EPGP with decay. This rewards people who attend most of the time over those who attend sporadically which I feel is only right. However, it gives the latter people fair chances at loot. The decay prevents someone from running a lot, not taking loot, then coming back after 2 months off and grabbing lots of loot from the people who've been there more often (which will feel unfair to the latter). It also acts as an incentive to spend GP on gear vs banking it for something off an endboss (which would mean that the raider is passing on upgrades and thus not helping the raid become more powerful).
Ultimately, if your raiders don't feel your system is fair, you're about to fuck things up. It doesn't matter that your officers love it if the people who raid hate it (and it very much doesn't matter what non-raiding officers think).