Libertine + pdftex: using 'Th' and 'Qu' ligatures with T1 font encoding
Based on karl's answer at Linux libertine, the {\l} character, ligatures, and T1 fontenc. Of course, in this case, the desired ligatures need to be explicitly invoked via macro.
\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage{libertine}
\newcommand{\Th}{\begingroup\fontencoding{OT1}\selectfont Th\endgroup}
\newcommand{\Qu}{\begingroup\fontencoding{OT1}\selectfont Qu\endgroup}
\begin{document}
I have Th and Qu but I need the ligatures \Th{} and \Qu{} too though.
\end{document}
This might not be the solution you are looking for but just using LuaLaTeX (or XeLaTeX) and OpenType fonts you don't have this problem.
\documentclass{scrbook}
\usepackage{libertine}
\begin{document}
Ligatures with \texttt{TU} encoding:
ff fi fl ffi fb fh fj fk ft Qu Th
\end{document}