I haven't decided for sure, but at the moment I'm leaning towards encoding them as DTS-HD MA rather than TrueHD, since while Dolby files seem to have greater playback compatibility, they are apparently more complicated to use correctly in Bluray authoring. But I think this should be investigated more thoroughly before I make a final decision on the matter.
As I understand it, TrueHD is only more complicated because it requires an embedded DD track for legacy system support, since it doesn't use a "core" arrangement like DTS-HD.
However, if you have a TrueHD track, I believe Eac3to.exe will decode the soundtrack and re-encode to DD plus embed it correctly in the file if you specify output.thd+ac3: it's only a single file.
Anyway, I expect either TrueHD or DTS-HD MA will be equally well supported on Bluray players: it's mainly mkv versions that often experience problems in media players due to the "generosity" of the studios influencing the manufacturers.