What you really want to look for is a barebone system. I use Asus barebone systems like the P4-P5N9300 with an add on parallel port card
http://www.asus.com.au/product.aspx?...MLgh6B4GRRCGDK
or T3-P5G43
http://www.asus.com.au/product.aspx?...qtErskUMIgZVDV

you still find older models (called AS V3, Google for it, they are excellent) with similar specs and the 775 form factor motherboard that have even integrated parallel ports so you can get quite cheap high performance chips to fit and good quality RAM to make a very good computer that will not run out of breath running your machine and do some design work at the same time. Some come with integrated graphic too and yes, they do work well too.
I got excellent results with the E 5200 and E7500 processors and can run the machine at 100 000 pulses with no problem what so ever. And I can do multi tasking too.
The barebone systems are rather small and I bet there are others out there performing as well or even better, for example the Shuttle range. So, why go for the Atom? Except it is an integrated system with touch screen and the ability to add a parallel port... Then I would be tempted. You know one of those new things that are all screen...