I've seen these discounts / websites mentioned more often than any others on this site:
1. "Stay More, Save More" (SMSM), booked through Universal Orlando or Loews hotel websites. Positives: they offer greater discounts the longer you stay (thus the name), they don't require prepayment, you can earn loyalty points from Loews or Hard Rock, and you get the peace of mind from dealing with the hotel directly. Negatives: can be more expensive than the other discounts below, but not necessarily.
2. "Annual Passholder" (APH), booked directly through Universal Orlando. Positives: very low rates, plus the benefits mentioned above. Negatives: at least one member of your party must have an Annual Pass by the time you check in. Also, rates only released a few months out.
3. Cheaptickets / Orbitz: two different version of the same website - Cheaptickets generally offers cheaper rates; Orbitz is slightly higher, but has a rewards program. Use the promo code listed on their home page (it changes each week, but they promote it freely) for very good rates. Negatives: often require prepayment, but this is usually refundable until a week or so before booking (check the fine print). You're not dealing with the hotel directly, but many, many people have used Cheaptickets without a problem.
4. AAA / AAA.com website: AAA members can call AAA travel agents for complete travel packages and advice, including park tickets, often at a good discount. The AAA website also has very good rates (they're frequently the best rates I've found anywhere - I've seen rates at aaa.com that were more than $100 a night less than anywhere else). Negatives: every state/region has its own website, and they can offer wildly different discounts and hotel availability, and sometimes the website rates are quite different from what an agent will quote you. Some (but not all) rates require AAA membership, and many require prepayment (usually fully refundable, again check the fine print).