Bloodhorse Stallion Register - Search by state, farm, stud fee and more. Each stallion comes with his own PDF file that gives all kinds of information about the stallion and his best offspring to date.
Bris Online Stallion Register - You can use their searchable stallion register for free, but you need to become a Bris member before they'll let you use it.
Equineline - The Jockey Club's online service. Offers an official stallion register.
Rancho San Antonio Stallion Connection - A very nice index of sires currently standing and links to their 'official' web pages. Also offers quite a few pictures and has stallions sorted in a number of ways. Not neccessarily complete, but still very nice.