How to manually equalize columns in an IEEE paper if using BibTex?

I have submitted to both ACM and IEEE conferences and the easiest thing for me has been using:

\usepackage{flushend}

I've heard it doesn't always work well, but it's been great for me

http://www.ctan.org/pkg/flushend

I went back to RTFM again, and it turns out this is addressed right in "How to Use the IEEEtran LaTeX Class" by Michael Shell (maintainer). Section XIV notes that IEEEtran helpfully provides the \IEEEtriggeratref{} command for just this purpose. By default, it fires a \newline at the given BibTeX reference number. You can even change the command to fire with \IEEEtriggercmd{}.