VLC has an export wizard with the features to do the cutting, but it's always a crap shoot as to whether it will actually work on any particular combination of input and output settings. AFAICT leaving "encode video" and "encode audio" both UNchecked means passthrough (no recoding); I use that about every other day on MPEG transport streams. As for rejoining the files in another order, ffmpegX has the features, but same caveat on them working.
QT Pro really is an ideal tool for this type of editing. Absolutely the best interface and implementation for it. If you ever plan to do this type of thing again in the future I say buy QT pro.