If you are getting a mid-tower, I'd recommend something like the Rosewill Redbone or Redbone U3. Building your own case can be a little tricky: making sure the airflow is sufficient, having enough space to properly mount all of your drives, making sure that the motherboard can be mounted properly. I'd go ahead and buy an inexpensive case rather than build one.

Only you can answer whether it would be cost effective, considering time required for design, materials and actually build a custom enclosure.