First, develop some patience. 20 minutes of contemplating never hurt anyone.
I like using Really Useful Boxes (found at Staples, Officemax, online) for building stuff into. Easy to work with material.
Try and mount all parts to the box, or to the cover. Minimize the number of wires that have to go to both.
Ribbon cables are good.
Panel Mount connectors for connecting up wallwarts are good.
Scroll down here, you can see some examples.
http://www.crossroadsfencing.com/BobuinoRev17/
Pencil cases can be useful too.
Be creative.
Also look at www.ponoko.com for customizing your design.
Sparkfun has a collection of little boxes too.