My PhD thesis in LaTeX:
http://dcc.ufmg.br/~lcerf/publications/PhD%20thesis%20(Lo%C3%AFc%20Cerf).pdf
If you like the theme (André Miede's work, not mine!), here it is:
http://www.ctan.org/tex-archive/macros/latex/contrib/classicthesis/
The structure is modular. I can send you the source of my thesis if you want
an example. Notice however that it does not rely on the usual way to divide a
LaTeX document into many files (the usual way is to use \input, which is like
C's #include).
My thesis does not show source code but much pseudo-code (the "algorithmic"
package was used). For real source code, other packages exist (something
called "listing" I think).
By "graphs", I believe you mean line charts. In my thesis, I used 'gnuplot'
to obtain EPS images, that I converted to PDF with 'epstopdf' (with the
'pdflatex' interpreter you cannot include EPS but you can include PDF) and
inserted with LaTeX's \includegraphics command. However, if you mean "graphs"
as in those at the bottom of page 123 of my thesis, then I use the LaTeX
package named "tkz-graph". And I used the "pst-tree" package for the trees
(such as the large one on page 65).
Pictures are inserted with LaTeX's \includegraphics command. Notice however
that the type of images you can include depends on the interpreter you use. I
used 'pdflatex' for my thesis and could insert PDF, PNG and JPEG. With
'latex', you could only insert EPS images. To make diagrams, you can use the
excellent Inkscape (something more to learn though), which can export to both
PDF and EPS.
And, of course, LaTeX rocks when it comes to writing equations.
