I've recently been experimenting with the Matroska container format (.mkv) for encoding. My reasoning is full support for features such as b-frames (without ugly hacks), Chapters and has much less overhead than AVI (on long runs, this can save up to 10MB from the end filesize).
I've already decided that for future runs that are greater than 40minutes I'll be using mkv, but I've also trialled chapters with Upthorn's Ecco 2 run. This allows the viewer to select certain parts of the run based on a chapter name (for example, the names of areas or levels that the viewer might be interested in). I've run into a slight problem though with compatibility.
Media Player Classic: Works fine, only uses chapter titles.
Windows Media Player: Works fine with Haali Media Splitter, only uses chapter titles.
VLC: whenever one chapter changes to another, the audio exhibits a slight pause. Also, selecting a chapter causes video to freeze for 5 seconds on the last frame. I'm unsure why, but I presume it's a bug in the demuxer. Full chapter/sub-chapter support otherwise.
mplayer: Works fine, only uses chapter titles.
The KMPlayer: Works almost perfectly. Chapter/sub-chapter support, but incorrectly detects chapters after sub-chapters as another sub-chapter, resulting in odd stacking in chapter context menu. Recommended.
Now to the point of my post: I'm curious if anyone is interested in chapters in long runs or not. Do you think it would be useful?
Edit: I'd just like to point out that all the above support mkv flawlessly. Any problems are to do with chapters.