Yes, there are good reasons I go overboard with anchors and hyperlinks. But you don't need to know them, so drop dead.
Just kidding.
All thinks considered, the Web is a second-rate hypertext system.
Ted Nelson, Godfather of the Web, Lord of Xanadu, and Coiner of Hypertext, insists that good hypertext has no point of view. Hyperlinks, according to Ted, are not endorsements of a destination or an attempt to co-opt a stranger's work; rather, they're acknowledgements of (and pointers to) a source of information for a given concept. The reader should only be shown where information is; they can analyze it themselves.
Nelson also thinks every word should lead somewhere, which just isn't practical these days -- you try coming up with a link for "a", "the", or "phelgmatic". Just doesn't work, does it?
To keep from driving myself insane, I decided to gratuitously hyperlink just the nouns, and made up The Rules (long before those other Rules), which hopefully put some structure back into a chaotic philosophy, so that readers at least have some idea of where a hyperlink will take them.
The names of universities, corporations, government agencies, and human beings link to their respective home pages (e.g. University of Toledo, IBM, Department of Labor, Michael Bauser).
In some cases (usually celebrities or college professors), these are links to pages about a person, rather than pages by a person (e.g. R.E.M.).
This is probably the most obvious rule (and one most people on the Web follow implictly, to some degree), but it's beginning to drive me up a wall, because I keep wanting to link first-person pronouns to my homepage.
Names of programs link to a page describing the program (e.g. Lynx), or more rarely, an ftp directory (e.g. metamail. Precise file names link directly to the files named.
UNIX command names usually link to the SunOS man pages (e.g. grep(1)). (Hey, they were there, you know?)
The names of nations, states, cities, etcetra, link to the first interesting page I found through CityNet, as for Boston, Massachusetts. I could have just linked to the CityNet entries, but that would have been too easy.
This rule is now causing me a fair amount of pain, as both my alma maters, the University of Toledo and Kent State University have devoted individual web pages to every single building on their respective campuses. I'm a little scared, thinking of where that's leading. What's next? A homepage for every dorm room?
The names of newsgroups usually link directly to that newsgroup (e.g. alt.culture.usenet, unless I've found a really good web page for the group. The first requirement for "really good" is that it includes a link to the group, so you're never more than a jump away.
Works of art, government documents, international treaties, and other aspects of material culture get a link to a page discussing them, except in those rare instances (mostly written works) where there's a web-accessible version.
Any hyperlink that isn't covered by the Rules is likely to be pretty unpredictable. Keep in mind, though, that I try to avoid links to index sites like Yahoo, and I consider Project Galactic Guide a standard reference work.