If you use Adobe Reader, then there is also pdfcomment. You can run texdoc pdfcomment in your terminal to read the manual. Like todnotes package, this package tries to emulate the commenting functionality found in some word processors.
This sample code is taken from the example.tex file provided with the package and some of the things that it can do.
\documentclass{article}
\usepackage{amsmath,array}
\usepackage[svgnames]{xcolor}
\usepackage{pdfcomment}
\usepackage{lipsum}
\begin{document}
\pdfmarkupcomment[author={Donald Duck},subject={Strikeout},color=red,markup=StrikeOut]{A little Test!}{Why is this repeated? This is a StrikeOut markup annotation}
\pdfmarkupcomment[author={Donald Duck},subject={squiggly},color=Teal,opacity=1.0,markup=Squiggly]{Unfortunately the support of pdf annotations by pdf viewers is only partly available to nonexistent. The reference viewer for the development of this package is \texttt{Adobe Reader}.}{This is a Squiggly markup annotation}
\pdfmarkupcomment[id=300,author={Donald Duck},subject={highlight},color=yellow,opacity=1.0,markup=Highlight]{Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Ut purus elit, vestibulum ut,
placerat ac, adipiscing vitae, felis. Curabitur dictum gravida mauris. Nam arcu libero,
nonummy eget, consectetuer id, vulputate a, magna. Donec vehicula augue eu neque.
}{This is a Highlight markup annotations with page break}
\begin{pdfsidelinecomment}[avatar=CaptainJack,subject={sideline},opacity=1,color=red,icolor=yellow,caption=inline,linebegin={/Butt},lineend={/Square},linewidth=3bp,linesep=1cm]{ ! Delete ! }
\lipsum[2-4]
\end{pdfsidelinecomment}
\vspace{2cm}
\definestyle{mathpopup}{author={},subject={},color=NavajoWhite,markup=Highlight}
\[
\begin{array}{c>{\displaystyle}c}
\text{Bernoulli Trials} &
\pdfmarkupcomment[style=mathpopup]{P(E)}{Probability of event E: Get exactly k heads in n coin flips.}%
=
\pdfmarkupcomment[style=mathpopup]{\dbinom{n}{k}}{Number of ways to get exactly k heads in n coin flips}%
{\pdfmarkupcomment[style=mathpopup]{p}{Probability of getting heads in one flip}%
}^{%
\pdfmarkupcomment[style=mathpopup,mathstyle=\scriptstyle]{k}{Number of heads}
}%
\pdfmarkupcomment[style=mathpopup]{(1-p)}{Probability of getting tails in one flip}^{%
\pdfmarkupcomment[style=mathpopup,mathstyle=\scriptstyle]{n-k}{Number of tails}%
}%
\end{array}
\]
\end{document}