I don't recall seeing what DVD player and receiver/processor/amp you're using. That info might help.
Something to keep in mind is that Dolby Digital and DTS are lossy formats. IMO you don't really gain anything by playing them back through the analog outputs of the DVD player because they aren't true high resolution formats to begin with.
It comes back to the quality of the decoders and the algorithms used to reconstruct the data. All else being equal, the decoders in most half-way decent receivers or processors will be better than what's in most DVD players. There will be some exceptions, I'm sure the decoders in a Denon DVD-5910 player are better than those in a JVC FX-10 receiver, but then again, no one who has a 5910 would be running it through an FX-10.
If you do have a top notch player and are going to use the analog outputs from the DVD player for DD/DTS playback, you want to make sure the downstream components will not degrade the sound quality. A good analog multi-channel preamp, like the Sony TA-P9000es or a McCormacK MAP-1, driving a good multi-channel power amp or 5 mono-blocks, would be ideal. OTOH, if you're going to run the analog outputs through a typical mass market HT reciever then you have not really gained anything, IMO.
But in the end the only way to know what will sound best to you is to hook it up both ways and listen.