In this video, Daniel Fisher, in-house synthesist at Sweetwater, does an in-depth side-by-side comparison of the Dave Smith Prophet-6 and OB-6. Sweetwater had this to say...
There are more similarities between the two synths than differences; but they each have unique features that may make one or the other (or both!) right for your music.
One important note: when the Prophet-6 is updated to OS Version 1.3.1 or higher, it gets two additional Flangers plus a Ring Modulator and a new Phaser, making the effects list of both the Prophet-6 and OB-6 much closer.
Since the sound engine for the Desktop Module versions of each synth are the same as their 49-key versions, this video is appropriate for all four products.