The iPad and an e-book reader by Moon allow one to choose from a short menu of font styles, but otherwise all one can do is adjust the size of the typefaces built into the book by the publisher on nearly all E-book readers.

I think you may be able to do it using the "fixed layout" epub format in iBooks on iPad/iPhone/iPod:

http://www.pigsgourdsandwikis.com/2011/02/fixed-layout-epubs-for-ipad-an...

That is all very well, but since some people insist on having something portable for reading e-books, it's still helpful to recommend to them that they buy the one with the ability to install one's own fonts - if one's goal is to encourage the whole world to use modified versions of fonts that help them to avoid... negative thoughts.

Of course, I don't think Adobe Reader lets me change the font on most .pdf documents, and so the choice of e-book format has a significant effect as well.

You can embed fonts in epubs as well.

Don't most readers just ignore embedded fonts and substitute built-in fonts?

Straight out of the box: Yes. With some extra effort: No.

The notion that the end user should be able to choose fonts isn't practical in all contexts, in fact: in most contexts it does not work at all.