I have only read a few fiction books that make brilliant use of footnotes.  One is The Brief Wondrous Life of Oscar Wao.  In that case the footnotes are a direct conversation between the narrator and the reader and instrumental to the story.  They are part of the story.

In Kiss of the Spider Woman, the footnotes serve the same way at some points.  In addition to providing information about theories on homosexuality in an objective way, they allow the author to speak directly to the reader.  Levine (cited in Wikipedia) described the author’s footnotes as acting “largely as a representation of Puig's political intention in writing the novel: to present an objective view of homosexuality” (Wikipedia).

Consider the following footnote from page 59.

“[Homosexuality] could be cured by means of injections to restore the hormonal balance” (p. 59).

In this case, the footnote searches for a biological reason for homosexuality, and interprets it as normal behavior.  Some of the footnotes support this belief, while others describe it as normal.  This contradiction forces the reader to pay attention and make his or her own determination.

Not all footnotes are from the direct voice of the author though.  Some are from another character, Anelli Taub.  The effect is the same though.  Levine notes that “footnotes tend to appear at points of the greatest misunderstanding between Molina and Valentin” (Wikipedia).

I think you will find the following teacher’s site helpful. 

http://mrhoyesibwebsite.com/Prose%20Texts/Kiss/Motif%20Tracking/Footnotes%20-%20Annie%20&%20Dev.htm

It includes several footnotes and an explanation of the progression of them.

Citations:

"Kiss of the Spider Woman (novel)." Wikipedia. Wikimedia Foundation, 03 Nov. 2012. Web. 07 May 2012. <http://en.wikipedia.org/wiki/Kiss_of_the_Spider_Woman_(novel)>.

Puig, Manuel. Kiss of the Spider Woman. New York: Knopf, 1979. Print.