.brf files are generated if the 'backref' or 'pagebackref' options of the hyperref package are enabled. These are intermediate files, so shouldn't be tracked.

Refer to the biblatex manual at http://ctan.unsw.edu.au/macros/latex/contrib/biblatex/doc/biblatex.pdf:

(p.106): The name of the additional aux files is the base name of the main input file with the string -blx and a running number appended at the end.
[...]
Apart from these aux files, biblatex uses an additional bib file with the same suffix to pass certain control parameters to BibTeX.
[...]
When using Biber, biblatex writes a control file named example.bcf and ignores \blxauxsuffix.

Note: the running number mentioned in the documentation is not always added to the suffix.

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.

See: http://tex.stackexchange.com/a/17846

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.