From the man page for latexmk (http://manpages.ubuntu.com/manpages/raring/man1/latexmk.1L.html):

[...] the -recorder option with latex and pdflatex. In (most) modern versions of these programs, this results in a file of extension .fls containing a list of the files that these programs have read and written.

Latexmk specifies this option in its latex commands and so produces temporary files with this extension in latex projects.

The [todonotes package](http://www.tex.ac.uk/tex-archive/macros/latex/contrib/todonotes/todonotes.pdf)
generates "tdo" files when you use the \listoftodos command.