Guys, around 4 years ago, I was using an online company that had a free PCB software that was integrated with the company system. So it would actually tell me how much the design would cost to run and let me order directly from the software. But I don't remember the name of the company, as I wasn't planning on doing any PCB designs...
Search the forum for "pcb" (search box at the top of any forum or Arduino.cc page. It looks like a google search but is limited to Arduino.cc.
There have been tons of discussions about PCB Software and Board Houses. It sounds like you are talking about someone like PCBExpress or Express PCB (can't remember which way it goes.)
I think you'll find most hobbyist try to stay away from a board manufacturer with proprietary software. Since you last designed boards four years ago services likes BatchPCB and SeeedStudio's Fusion service have popped-up. They basically charge flat rates (or easily to calculate rates.)
For small boards, it looks like the current trend is to use EagleCAD design tool (free version "EAGLE Light" adequate for Arduino shield-sized boards) which can create industry-standard Gerber RS-274x format files. http://www.cadsoft.de/freeware.htm
From there you can use one of the services that batch together boards to avoid the normally high setup fees.
As an example, the BatchPCB service offers 2 layer boards, 8/8 mil rules, at $2.50 per square inch with $10 setup fee. Average delivery in 3-4 weeks depending on volume of other orders. http://batchpcb.com/index.php/Faq
The PDX-Dorkbot PCB Group order may be the cheapest I've seen, at $5/square inch but you get 3 copies of the board, with no setup charge, and free shipping(!) 2 layer boards with 6/6 rules, soldermask both sides, silkscreen both sides. Eagle design rules available. They only do batches at intervals; the next one listed to go out 8am PST October 25th 2010. http://dorkbotpdx.org/wiki/pcb_order
Another alternative based in China, pricing in Euros, offering 14 or 10 business days for production. 0.2/0.2mm rules (8/8 mils). Online form for price quotes, 2 layer up to 10 layer PCBs. http://www.makepcb.com/
iTead Studio in China, $25 for 5x5 cm board, 10 copies. 6/6 mil design rules. Various shipping options. Reportedly they use the same fab house as SeeedStudio. http://iteadstudio.com
$12 for 5x5cm and $28 for 10x10cm. Can't beat this with a 5-ton stick if you tried, unless you order 1000 boards from somewhere.
As stated though, this is only really beneficial if you could use 10 boards. Otherwise I believe the best pricing for 3 was dorkbox.
Yes it is reported iteadstudio uses the same pcb house as seeedstudio. I couldn't find much info on them but last week I decided to give them a try. I'll post a thread with pics when I get my boards in. They did supposedly ship 2 days after I placed the order.