Just to add to the comments of the other posters. Just add packages as you need. A thesis preamble is bound to expand fast. Divide it into sections such as General, Typography, Mathematics, Commands etc. As the preamble grows some of these you will pass to a package say moremath.sty.
Keep the style simple, no fancy fonts. Under typography you can include microtype and stmarysd. Under mathematics you have included the basis and I will second Mico's suggestion of mathtools. Under commands put all your specials. For example under theorems you should include all your formatting decisions as well. As a bonus, here is some styling for theorems.
%% Theorems formatting
\newtheoremstyle{itheorem}{}{}{\itshape}{}{\bfseries}{.}{ }{#1\if!#3!\else\ \fi\thmnote{#3}}
\newtheoremstyle{icorollary}{}{}{}{}{\itshape}{.---}{0pt}{#1}
\newtheoremstyle{numcorollary}{}{}{}{}{\itshape}{.}{ }{#1\if!#3!\else\ \fi\thmnote{#3}}
\newtheoremstyle{idefinition}{}{}{}{}{\bfseries}{.---}{0pt}{}
\newtheoremstyle{ilemma}{}{}{\itshape}{}{\bfseries}{.---}{0pt}{#1\if!#3!\else\ \fi\thmnote{#3}}
\newtheoremstyle{iother}{}{}{\itshape}{}{\bfseries}{.---}{0pt}{\thmnote{#3}}
\theoremstyle{ilemma}
\newtheorem*{lemma}{Lemma}
\theoremstyle{itheorem}
\newtheorem{theorem}{Theorem}
\theoremstyle{iother}
\newtheorem{other}{}
\theoremstyle{icorollary}
\newtheorem{corollary}{Corollary}
\theoremstyle{numcorollary}
\newtheorem{ncorollary}{Corollary}
\theoremstyle{idefinition}
\newtheorem*{definition}{Definition}
\newtheorem*{definitions}{Definitions}
\newtheorem*{defnorder}{Definition of Order}
%% Proof environment
\renewcommand{\proofname}{\upshape\bfseries Proof}

Keep the style simple and clean with minimal bold and don't use the standard LaTeX class.
t1enc(use\usepackage[T1]{fontenc}instead). And it would be better to use packages like geometry or typearea to setup text area and margins. At least better use\setlengthto set lengths instead of using low level TeX. – Schweinebacke Nov 08 '11 at 16:00