There's no difference between the uncut DVDs and the stuff you get from fansubbers, other than the translations.

There's several differences between the uncut DVDs, and the episodes as they air on television. The openings/endings are different. Some of the blood is edited out, and yes, a couple scenes are clipped. Much less so than with most anime, but still, there are cuts. Some for violence, some for sexual content. For example, underwear added to the Sexy Jutsu. Or Anko's scene where she stabbed the kunai through her own hand into Orochimaru's into the tree, being clipped to basically just show the pained expression on her face, etc.