Gosh! Your options are almost limitless.
First, it depends on how much you want to spend. It can range anywhere from $65 - $365 per night. Be certain about what type of stay you want. Some people expect the Hyatt experience at a Travel Lodge price (both chains have a hotels in the vicinity).
Shuttle Options - I've found it much easier NOT to rely on a shuttle service, whether it's provided for by the Hotel, or by The Anaheim Resort Transit, because you need to apply to their schedule. So, typically, I choose a hotel that is right across the street so I can walk. There are exits from the Parks on the East, West & South. So, anything with-in a block is close.
Bikes - Of course, you can always bring your bikes with you, and lock them up right by the Security check points. We've done that before. The bikes are actually quite safe (even Disney employees lock up their bikes there). Why a bike? Well, you can venture to a hotel that is a couple of blocks away, and your only riding for 2-3 minutes (very fast).
Breakfast - Also, most hotels have some sort of breakfast - granted, most of those are rather pathetic (coffee and a cheap danish - you'd be better off going to the store and buying your own). There are (of course) other places to eat, but they charge a slight premium because their right next to the Parks.
Other Food - one other thing you may not have thought of, if you're trying to save on money, is that you can bring your own food into the Parks - with-in reason of course (Like no glass containers).
Otherwise, I always stay at a little cheap motel literally across the street - del Sol Inn, it's cheap and clean - plus they have those cheap danish!