Apple's RAM promo makes it a much closer call -- for example, buying a dual 1.8 G5 with 4GB RAM from Apple: $3,549 (normally $4,249). Buy a dual 1.8 from macconnection then install crucial RAM to upgrade to 4GB: $3,445.89 (more than $100 less) plus you can ebay the 2 modules of 256mb you take out, and if you're from CA you save on sales tax (about $280, not to mention other rebate offers for free printers and stuff).
Bottom line: even with an academic discount and the memory promo, someone in CA is still better off buying normally from macconnection.com (or macmall or any of the others, probably...) When the memory promo ends, it's not even close.