This document style introduces vertically spacing between paragraphs, thus giving too much space before proofs, and uneven spacing around theorems, etc. Redefining the internal commands of amsthm, putting negative space into \topsep of the proof environment, and making theorems start with with a \parskip and end with no spacing gives the following result with reasonably uniform spacing:
\documentclass[paper=a4, twoside=true, openright, parskip=full, chapterprefix=true, 11pt, headings=normal, bibliography=totoc, listof=totoc, titlepage=on, captions=tableabove, draft=false]{scrreprt}%
\usepackage{amsthm}
\makeatletter
\renewenvironment{proof}[1][\proofname]{\par
\pushQED{\qed}%
\normalfont \topsep-6pt
\trivlist
\item[\hskip\labelsep
\itshape
#1\@addpunct{.}]\ignorespaces
}{%
\popQED\endtrivlist\@endpefalse
}
\def\th@plain{\thm@preskip\parskip\thm@postskip0pt\itshape}
\def\th@definition{\thm@preskip\parskip\thm@postskip0pt\normalfont}
\def\th@remark{\thm@headfont{\itshape}\normalfont\thm@preskip\parskip\thm@postskip0pt}
\makeatother
\newtheorem{lemma}{Lemma}[chapter]
\theoremstyle{definition}
\newtheorem{definition}{Definition}[lemma]
\theoremstyle{remark}
\newtheorem{remark}{Remark}[lemma]
\newcommand{\thesisTitle}{The Clean Thesis Style}
\newcommand{\thesisName}{Ricardo Langner}
\newcommand{\thesisSubject}{Documentation}
\newcommand{\thesisDate}{February 1, 2012}
\newcommand{\thesisVersion}{0.2}
\newcommand{\thesisFirstReviewer}{Jane Doe}
\newcommand{\thesisFirstReviewerUniversity}{\protect{Clean Thesis Style University}}
\newcommand{\thesisFirstReviewerDepartment}{Department of Clean Thesis Style}
\newcommand{\thesisSecondReviewer}{John Doe}
\newcommand{\thesisSecondReviewerUniversity}{\protect{Clean Thesis Style University}}
\newcommand{\thesisSecondReviewerDepartment}{Department of Clean Thesis Style}
\newcommand{\thesisFirstSupervisor}{Jane Doe}
\newcommand{\thesisSecondSupervisor}{John Smith}
\newcommand{\thesisUniversity}{\protect{Clean Thesis Style University}}
\newcommand{\thesisUniversityDepartment}{Department of Clean Thesis Style}
\newcommand{\thesisUniversityInstitute}{Institut for Clean Thesis Dev}
\newcommand{\thesisUniversityGroup}{Clean Thesis Group (CTG)}
\newcommand{\thesisUniversityCity}{City}
\newcommand{\thesisUniversityStreetAddress}{Street address}
\newcommand{\thesisUniversityPostalCode}{Postal Code}
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}
\usepackage[figuresep=colon,sansserif=false,hangfigurecaption=false,
hangsection=true,hangsubsection=true,colorize=full,colortheme=bluemagenta]{cleanthesis}
\begin{document}
\pagenumbering{arabic} % arabic page numbering
\setcounter{page}{1} % set page counter
\pagestyle{maincontentstyle} % fancy header and footer
\chapter{Test}
\blindtext
\begin{lemma}
A lemma.
\end{lemma}
\begin{proof}
The proof.
\end{proof}
A line of text across the page to demonstrate some spacing effects of
the spacing changes.
\begin{lemma}
Another lemma.
\end{lemma}
\begin{definition}
A definition.
\end{definition}
\begin{remark}
\blindtext
\end{remark}
\end{document}
