Alternatives to commercially available flow cytometric analysis software for use in cell cycle analysis?
Sounds like you should look into Bioconductor's flow suite.  I actually really like doing flow analysis in R, but it takes some practice and getting used to.

The biggest problem you will run into (in my opinion) is gating.  It's not easy to setup a GUI point and click gate.  Rather, you'll be more forced and inclined to set limits with algorithms or hard value limits.

I found .Net Bio to be fun, but not nearly as powerful as Bioconductor.

Meta note, couldn't think of a less opinion oriented way to answer other than just to say "It can be done in R utilizing Bioconductor."  If this is still off, I'm fine with deletion.