If you're a smaller guild, be very careful who you ally with. Often times less scrupulious guilds will form alliances with every intention of enticing your mates to join their guild. I recomend establishing a "No poaching" agreement where each guild agrees to a "cooling-off period" where former members of an ally guild can not be invited to guild without the former guild's consent. This goes a long way to ensure ppl aren't making hasty decisions to leave your guild because they think they have a home with your ally. The first time there's a serious violation of this agreement, inform your members of the other guild's bad conduct and break the alliance.
Note: with such an agreement, it should be standard recruting procedure to ask a potential recrute if they were in the ally guild during the agreed cooling-off period. Liars should be kicked, period.
Individual participation and favoritism can be a huge issue. On those occasions where more than 24 ppl want to raid, you'll need to be careful to ensure members of one guild aren't in/excluded due to raid leader bias. Likewise for any assigned loot, quest updates, etc.
Loot is always a HUGE issue in an alliance. Be sure to setup a system that doesn't favor one guild more than the other and be sure whatever tracking that requires is supervised by both guilds. Your joint tracking system should only track events where both guilds have an equal opportunity to participate.
Profit and expenses need to be monitored. Often times a small number of ppl end up with all the trash loot, which can amount to significant cash. The cash generated by this trash loot should pay for any expenses for the raid (potions, repare kits, regents, etc) and any net profit should be divided between the guilds. Don't make the mistake of pooling this profit in one bank. If/when the alliance breaks up, you'll have far less issues if nothing needs dividing.
Always follow the old rule, hope for the best and plan for the worst. Assume from the start the alliance is temporary and plan accordingly. If it lasts forever, great. If not, well you'll be happy you planed ahead. And remember, there's no devorce court in EQ2