It has been a while since I actively used TeX and encountered interesting issues, but as the work on my Master thesis has finally started I am again TeX'ing. It feels great!

The todonotes package is a great tool if you're as disorganized as I am, whenever I have a random idea, or don't feel like finishing something or don't want to add the correct citation, etc. I add a \todo{} and postpone the work. Postponing is good.

And if you can postpone work in a fancy way it's even better! So I've got 5 "categories" of notes, each with its own color and options. An example (click for pdf):

The interesting part is that I'm using the xparse package, to have optional commands. So I can choose between \addreference and \addreference{to that particular book for which I don't feel like creating a BibTeX entry right now}. It's really easy, just put 

\usepackage{xparse}

\DeclareDocumentCommand\addreference{g}{\todo[color = blue!30]{Add reference\IfNoValueF{#1}{: #1}}}
\DeclareDocumentCommand\checkthis{g}{\todo[color = red!50]{Check this\IfNoValueF{#1}{: #1}}}
\DeclareDocumentCommand\fixthis{g}{\todo[color = orange!50]{Fix this\IfNoValueF{#1}{: #1}}}
\DeclareDocumentCommand\expand{g}{\todo[color = green!50]{Expand\IfNoValueF{#1}{: #1}}}
\newcommand\removethis{\todo[color = yellow!50]{Remove this?}}

in your preamble when you have todonotes loaded. Adding the option textsize = small to your \usepackage command might be a good idea, and there is colorinlistoftodos if you want colored boxes in the list.