The new hotness in the Emacs community is revolving around Org mode.
Org is a fully featured planner and task manager, based on the outline-mode already present in Emacs.
But you don't care about those features, you're interested in Latex. Well, org can do Latex too.
For a document as simple as
# Header for proper HTML export -*- org-export-with-LaTeX-fragments:t -*-
* Chapter 1
You can tweak the preamble by modifying org-format-latex-header.
Links are as simple as [[http://orgmode.org][org-mode]] like a wiki.
** Subsec 1
* Chap 2
Stuff
** Subsec 1
\alpha doesn't need math-mode.
If $a>2$ and $$b=\sqrt{\beta}$$, jump for joy.
And
\begin{tabular}{lcr}
\hline
A & simple & table\\
\hline
\end{tabular}
You can export the whole thing in latex or HTML (if you have dvipng).
Exporting is as easy as
C-c C-e h = HTML export in the current directory - you get a free TOC.
C-c C-e l = Latex export to a buffer, in which you can switch to and C-c C-t C-p for pdflatex mode and then C-c C-c for export. - Another free TOC.
See the sections at http://emacswiki.org and http://orgmode.org for more info.