If you don't do gaming, you can also get a board with on board video /audio. I use these for the office with no issues. Of course we don't listen to Wagner here.
A couple of thoughts:
I just upgraded to 8gm ram and I find the difference more than noticeable.
I assume you have a screen, but bigger screens are pretty affordable these days.
Considered SSD?
If I were getting a new toy, it would probably be a new pen input pad.
I have a Cooler Master case with clips rather than screws. I can clip off the side panel or slide out the drive bays. Nice.
I suspect there are no video cards or boards without HDMI, but you should definitely get it.
Front bay card reader, if not provided.
Front bay USB panel if not provided.
I love Vacunita's list and like the others. You an also get a leg up on costs by picking up a "kit" from Tiger or Newegg: I've resorted to Tiger's salespeople in the past, and they have never steered me wrong.
I'd go I7 on the drive. I generally find after I put something together based on current standards that it is out of use in two years at the most. (I mean by that that, if I want to change something, I need to get all new components). Ergo, go with the newest.
You'd have to buy the parts there, but if you are in the Bay Area, Central Computing does a good job of putting the pieces together. I tend to get boneheaded and do it myself, then wonder why I didn't give it to them. Fry's surely does too.