for both
if you download autox264 AND applications pack (first post) when you start the application, it will find automatically the new decoding/encoding capabilities
in case of use avisynth (dgavcdec or ffmpegsource or dss) mencoder is used only for audio encoding, while autox264 will build a minimal avisynth script (crop/resize/denoise/filtering as requested, and of course decoding with dg/ff/dss) and will encode with x264
it works for linux (under wine) too
BHH