I'm a graduate student in mathematics but I've done a lot of open source software projects, some of which have even won hackathons. My question is should I put them on my CV? I've seen academic CVs only contain publications, conferences etc. But, I feel that these projects are very valuable to mention.
You're correct to want to mention them, CVs often probably only lack them because the writer hasn't done them or it isn't relevant to their career (perhaps they do not need to mention them any longer to prove particular skills). My CV included my programming/computing experience and was well received as the programming I had done was relevant; I was applying for computationally demanding PhD programmes.
Relevance is key so when including the projects, make sure the skills you gained from completing the open source projects are clear to the reader. Make sure it is also clear how these same skills are relevant to your application.
I am a mathematics professor and I served on a hiring committee this spring so I've been reading a lot of CVs recently. If the software projects that you have been working on are completely unrelated to your research or mathematics in general, then I would leave them off. If he projects are directly related to your research or even just mathematical in nature (e.g. Work on the Sage computer algebra system), then I would include them.
On my CV, I try to list software twice: once as part of a scientific project ("I studied ... and wrote a software tool to allow other scientists to ...") and once as a software project ("SequenceMatrix is a Java application to ... that I developed while working on ..."). The first includes scientific outputs, such as publications, findings and point to research interests, while the second includes development tools, software design and engineering practice. Which one I emphasize -- and whether I drop one entirely -- depends on what I'm applying for.