The first thing I thought of when you say mark many time points, is a Subtitle sync, or subtitle creator, as they need to do that same thing to determine in and end points for subtitle display. they also output a SRT file that is mostly human readable adjustable and editable. Most of them will allow loading up the video itself, to get the time code.
Then I tried to find one that would just set the sync points, so a person could add the text later, but I did not get too far. http://sourceforge.net/projects/subtitlecreator/ This one has a cool babe in the picture :-) so it must be worth trying.
this one claims to be able to make them from scratch http://easy-subtitles-synchronizer.software.informer.com/ probably a better choice.
If your trying to find cut points, or fades, virtual dub can do that automaticly and it is adjustable. Vdub won't write down the locations, just quickly find the next cut or fade. It does have the ability to save the list of cuts, to apply to another video the same way, but the data it saves is not simple. it also is adept to programmers adding things to it.
http://www.virtualdub.org/virtualdub_filters.html Also has some sub plugin.
Every pro editing package will export an edit list in various formats, for working with proxies, or to finish the actual editing on a film machine, or other equiptment or programs.
If you need to split the video up into pieces based on time code, cuts or fades, "scenalyser" or is it scenealizer would do that, even export clips, for rearanging. it also can make a list of where it thought scene changes and fades are. Then it can apply that list to the video.