Having trouble? Don't "get" the site, much less the jokes? Read on.
The idea of a mark-in is to act as a "bookmark" in the episode. Imagine that you're reading through the quotes of an episode that also features a short — The Ring Of Terror, for example, includes "The Phantom Creeps (Part 3)" near the end of the episode. There is, conveniently enough, a mark-in noting that the short begins at 01:15:08. This lets the reader know quotes listed after that mark-in are probably from that short.
A mark-in is nothing more than a time index (HH:MM:SS) and a brief description. If you browse through the existing episode mark-ins, you'll see typical entries denote when shorts begin, host segments, Invention Exchanges, and the like. Use these as a guide when deciding whether or not to add your own mark-in.
The episode pages let you download a copy of all the annotations as an SRT file. What is this? It's a simple file format for subtitles, allowing you to get the benefits of MST3K annotations as you watch the episode.
ffdshow, the popular playback codec for Windows, has the built-in ability to read SRT files; it's certainly not the only one, though.
(If you have information on playing back subtitles under other platforms, let me know and I'll add the appropriate information.)
Tags are quick, easy ways to categorize things with some brief, cross-referenced text. You can add many tags to quotes, and the same tag to multiple quotes. Some things to consider when adding tags:
Tagging items in a sort of ad-hoc categorization scheme is not a new idea. However, we blatantly ripped this implementation off of two popular services — Flickr (online photos) and del.icio.us (shared public bookmarks).
The main difference between them is that we use comma (,) separated lists of tags, and that anyone can tag any quote. The end result will hopefully be the same, though: fine-grained control over classification, community-wide input, and easy cross-referencing.