As I wrote about in my previous blog post, one of the reasons that we are developing our own STaM fonts is to better handle the various unusual letter forms in Tanach. Examples include the enlarged bet that begins the Torah, the enlarged ayin in the word שמע, the small alef in the word ויקרא, and the inverted nuns in Numbers 35. It would, of course, be a lot of work for me to research all of these unusual letter forms, were it not for a number of very thorough papers that have been published on the subject. So if you are interested in the subject, here are the links to resources that I have been using:
Typographic details in the Hebrew Bible (Andries E. Brouwer): This paper collects examples from many different sources, and provides extensive, categorized lists of unusual letter forms.
Typesetting the Holy Bible in Hebrew, with TEX (Yannis Haralambous): This paper is concerned with typesetting Biblical text, and provides lists of typographical oddities and how to typeset them using the TEX system.
Also, this chart list all of the unusual letter forms just in Torah: טבלת השינויים בספר תורה (הראל לוי)