I think for my digital archive I'll add the WOTW and Visitor tracks where they belong. If I don't go the whole hog and sort everything into episode order.
I just got done doing that yesterday! All the DS9 on CD I own in one folder in chronological order. (Emissary, Best Ofs, 4CD, James Darren album) ...137 tracks.
I actually much prefer it this way, as it breaks up some of the repetition people were talking about.