Most ePub, FB2 and MOBI ebooks come with a TOC. Some older MOBIs don't have a TOC but instead have an internal list of links to chapters near the front of the ebook.
I assumed that HTML and other less ebook-centric formats would not have a TOC, but in fact the two I tried both came up with a TOC using Desktop FBReader and OpenInkPot. I think FBReader is keying on HTML heading tags to automatically build a TOC.
One of the best features of FBReader is the Next Section key binding, which takes you to the next "section" which is usually the next entry in the TOC. This is particularly good for collections of short stories. There is also a Prev Section option. I use this so frequently that it is a real pain to read ebooks without a TOC.
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