In general, graphics that were censored will usually be uncensored or less censored if it's an ecchi series. If SHAFT made it, scenes will be retouched for quality. Other studios might also do retouch some stuff if they received complaints from the viewers. If it's a reference show, the direct references bleeped out on TV will not be bleeped out any longer.
Apart from the last episode being released on DVD only, I couldn't find any differences mentioned. Ecchi series and SHAFT releases are the ones that are most likely to have a better DVD release in my experience. (Edit: Better in terms of material. Quality of details will usually beat TV recordings even at higher resolutions.)