The things that I remember are:
The "free printer" rebate. If you purchase from Apple, you get a free printer, up to $100. You pay for the printer, then submit an online rebate and they mail you a check back for $100.
You also have the ability to sign up for a One to One membership only if you buy from Apple.
They also do educational/gov't discounts, as well as discounts for a few big businesses.