Ever notice how it now takes a year for Acrobat Reader to load up? You can speed it up about 20x or so, by moving the plugins you don't use out of the "startup" folder. If you put the files into the "optional" folder, I believe it will still be able to find them when you want to use them, and it will load them then.
A reasonable default is to leave ewh32.api, search.api, and reflow.api in your plugins directory, and move everything else into the optional folder.
You can make a disabled_plugins directory if you want them to be really gone.

Since I just wasted a bit of time trying to figure out how I had configured Cygwin the first time, so as to help someone else set up their account, I figure I will post the instructions here:

Scott Hansma originally wrote a plugin for Eudora in 1997. When he graduated, he asked if I wanted to take over control of the source, as he wasn't interested in working on it any more.