I ordered got both of these the Season 1 & the Crystal Empire DVDs. Season 1 features all the episodes from the first season plus several audio commentaries. The Crystal Empire features the Season 3 two parter plus 3 episodes Sonic Rainbow, Luna Eclipsed and It's About Time which is spread across season but all are great standalone epsidoes.
I've watched all of the Crystal Empire DVD and am working my way througb Season 1 again in DVD form. The audio commentaries are interesting as well.