Sometimes you can get them on Amazon.com through the "subscribe and save" feature for less. Just have to compare to other sources to make sure it's less.
Don't know if you are close to any universities, but when I was in grad school, our cycling team (club not varsity) got to make bulk orders at 50% cost once a quarter. We all loaded up with multiple 48 count cases. I'm sure we weren't that special, so GU probably does this with a couple of colleges.
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Another option is REI, who has a discounted price for when you buy more than a certain amount.
Pretty sure HEED sells a big (36 ozs) bottle of gel, which you could fill a gel flask with.
Occasionally I will see AccelGel's discounted on BonkTown.
Otherwise, I wait for the 20% off coupon from TriSports.