For me, build-to-order is the way to go. The pre-configured G4s don't suit my needs as a print and web designer — I do extensive work in Photoshop, Illustrater, Quark, Dreamweaver, etc. With the Apple Store I get flexibility that third-party vendors can't provide: I get what I want and discard the rest.

I chose a 500mhz MP G4 with a 64MB/30GB/Zip/56k/DVD-ROM configuration -- I don't have it yet, but that's the topic of another thread. I saved a few hundred dollars by getting an extra 256 MB of RAM through www.crucial.com for $294. By comparison, Apple charges $450 for a 256MB DIMM; MacWarehouse charges $600.

My point is to do what works for you. If you find that a preconfigured G4 will suit you, then by all means take the free RAM, free shipping, or whatever carrot they dangle and go with the third-party folks. But do your homework! Unless you're a video editor, do you really need DVD-RAM? (want=yes, need=no) Do you want to pay more for memory? If you can get your machine cheaper by stripping it down and filling in the gaps yourself, then why not do that?

As for the Apple Store you need to read the fine print to note there is no way to cancel or change an order once it is placed, unless you you contact a sales rep. by phone only no email (some internet company), which is 45 minutes on a great day. Around new product announcements time forget it. And that the Apple doesn't accept any returns period. I ordered an imac it was on back order for 6 weeks, then MacWorld came around and try as I might I couldn't get a hold of anybody to cancel or change my order by phone. Then they decided to ship it the day before the new models came out and to post my now obsolsete computer for $300 less before I actually recieved it. Sorry no returns! was the reply I got 2 weeks later when I finially got through after spending 40 hours on hold over the course of 4 weeks.
As an officer of the local Mac user group (which I strongly suggest you join one near you) I've heard countless horror stories about the local dealers. Mostly no service after the sale. Talk is cheap. You need to deal with someone you can trust and get a hold of when needed. The big retailers like Sears don't know what a Mac is let alone be able to answer any questions. Again this is another benefit of joining a user group - support. I usually buy from Outpost for price. Powermax and Small Dog are both excellent if you need hand holding and would bend over backwards to solve a problem, and do thier own repairs.

Many years ago I ordered a Performa 5200 from the Apple Store (Eduation). The computer arrived the day before the letter telling me my order would be delayed a week.