Picture Quality
Blimey, you think all decoders work exactly the same way? The quality of decoders varys enormously.
Some chips will cut certain corners, others chips will apply additional post processing to positively enhance the picture. HDMI ensures the output from the player is carried to the TV without degredation, it doesn't make all the players produce the same output in the first place. Software decoders (such as on the PC and the PS3) don't have the luxary of dedicated hardware and thus very often have to cut corners.