I use stereo (specifically upsample with my 990) for two-channel music. DVD-A and SACD, of course, don't get any processing.

For TV and movies, I use Pro Logic IIx-Movie (when the source is PCM stereo or Dolby Digital 2.0 it is used by itself, but when it'd a Dolby 5.1 source I apply Pro Logic IIx-Movie on top of Dolby 5.1 because I have a 7.1 speaker setup). If a disc includes a DTS track, I most often use it (with Pro Logic IIx unless it's a DTS ES track). Flagged Dolby EX tracks force EX decoding, but otherwise I use Pro Logic IIx.