Hello.
First, I apologize for the late reply. I've been swamped with meetings
and work the past couple days.
Create the following document (name it something like bibtest.tex):
\documentclass{tufte-handout}
\begin{document}
The only bibliography entries that appear are those which are
cited.\cite{Tufte2006}
\bibliography{sample-handout}% this points to the .bib file
\bibliographystyle{plainnat}% this is the citation style you want to use
\end{document}
Copy the sample-handout.bib file over to the same directory as your
bibtest.tex file.
Now run the following commands:
pdflatex bibtest
bibtex bibtest
pdflatex bibtest
pdflatex bibtest
The first pdflatex run will generate a bibtest.aux file. This file
contains (among other things) the keywords of any citations you
included in your document (i.e., any \cite commands).
The bibtex command will read the bibtest.aux file, extract any cited
publications from the database in the sample-handout.bib file, format
them according to the indicated \bibliographystyle, and put the
results into in the bibtest.bbl file.
The second pdflatex run typesets the bibliography entries.
The third pdflatex run checks the citation numbers and updates any
page references and links that may have changed during the previous
run.
The end result should be bibtest.pdf which includes the citation for
Beautiful Evidence.
(I've attached the bibtest.tex and sample-handout.bib files.)
If this doesn't work or you still encounter problems, please let me
know. Once we know that this test file works okay, we can compare it
against your .tex and .bib files to track down the problem.
Thanks!
--Kevin Godby