Yes custom system is usualy better and cheaper then prebuild systems.
As for recomended parts you should go for I7 and x58 board and 6/12GB ram as solidworks can eat up memory and CPU. I am not sure if current version of solidworks support or plan support GPU computing but if it do, 5870 could help with performance.
As an SolidWorks/Inventor user this is the best $1200-1300 system I can recommend right now:
CPU: Core i7 920
* The HT really helps here
Motherboard: P6T SE
* Solid motherboard for the price
RAM: Any quality 3*2GB DDR3 1600 kit will do
* SolidWorks can benefit from 12GB depending on what you do.
HDD: 2x Samsung F3s 500GB
* One of the fastest HDDs out right now
GPU: ATI 4670 or or 5750 (or higher if gaming)
****Very important: I'm assuming you are just a student and will not be doing any serious pro level designs. If you are a pro (as in this is your job), I highly recommend you looking in to a workstation card.
Case: HAF 922, Antec 900 or any other case with good airflow and space
PSU: Corsair 650TX or other quality PSU
* NEVER skimp on the PSU. Always get a PSU from Corsair, OCZ, Antec, PC Power & Cooling, or SeaSonic.
CPU Cooling: Core Contact Freezer with LGA1366 bracket
*I'm assuming you will overclock now or down the road.
@xrodney: SolidWorks dosen't use OpenCL or CUDA type accelerations currently. HOWEVER, you CAN benefit from a workstation GPU. The 5870 won't benefit when it comes to CAD work most of the time.
I am not sure if it is worth the cost difference though- what do you think? my budget is 1300-1600 so I could afford a card in this range if it made a meaningful difference. I am running assemblies with around 200 parts.