Like Static said, it's just different features. I have a Les Paul Special II that is labeled Custom Shop on the back because it has a flame maple veneer top. Its MSRP is only $20 more than the non custom shop version.
I have a "Custom Shop" Epiphone '61 SG Special, a faithful reissue of the 1961 Special, right down to the almost non-existent neck joint. It's a super cool guitar, features-wise, but it's no better or worse than any other Epiphone.