Batch video editing software that can trim without re-encoding
If you can script yourself, all you need to do is call FFmpeg repeatedly:

ffmpeg -ss [start-time] -i input.mp4 -c copy -t [clip-time] output.mp4


Here, start and clip times can be in the form HH:MM:SS.mmmm, or just in seconds. 



To give you a rough idea how that'd look like in Ruby, see this Gist of mine. It contains a script that takes an edit list, a folder of videos, and cuts them accordingly. I've used it very often for cutting videos based on an input edit list.

The edit list would look like that, with the timestamps in the proper FFmpeg format (e.g. 00:00:24.240) and the difference passed to -t in the last column.



Note that you can't expect it to work with any input/output without synchronization issues. If that's the case, you need to re-encode video and audio parts. I wouldn't use that script of mine though as it's not very … eloquent in that regard. Rather cut your video in a NLE.