secretbum, you're in Australia, some of the other posters are in the U.S or Canada. That makes a difference as far as price/discounts go. Of course the OP is in Australia too, but I think the discounts work out about the same if you're talking about percentage of purchase price/total value of the discount rather than dollar value.
If you're buying BTO, going with the online Apple Store probably makes the most sense, but it's not a requirement as Apple Stores and resellers can order BTO machines for you.
All of my Macs have been stock machines and I've purchased two of them from a reseller, and one from The Apple Store. I prefer to buy from a real store, partly because I'm impatient and don't like to wait for shipping, but primarily because I like to support local business and local employees. I would actually choose a reseller over the Apple Store in general but only campus resellers (like school bookstores) and the Apple Store can give the educational discount. I also feel better about support having purchased from a real store, although at least with Apple there's really no difference.