This is a very subjective question, everyone have their own individual preference when it comes to stuff like that. In my opinion, windows and linux both have their own strong point and weakness, well I would say Windows is more user friendly, as is mostly in graphical user interface, while Linux you will need to have strong knowledge in all the command as is more towards command line interface. I would totally agree going on the one that you will feel more comfortable with it since it would be a long running process.
Perhaps you might want to read more on this knowledge base article regarding on performance tuning for JIRA : https://confluence.atlassian.com/display/JIRAKB/JIRA+Performance+Tuning
i know this can cause some discussion but my personal opinion is...
if you want to host with performance and stability you will want to use linux.
it may be that some users have good experience with hosting on a windows system but let me guess...the majority runs unix based systems
I think the general answer is simply "what they support". However, I've seen strong suggestions that PostGreSQL is the preferred database (with MySQL second and Oracle a distant third). The preferred operating system is by far Linux (but that goes for almost everything nowadays), with hints that Red Hat and CentOS are the preferred distributions. This is just my impression though, I'm not Atlassian.
Perhaps better would be to test which one runs better for TomCat webserver. Here is a research report
In my experience they are both very comparable, with linux having slight edge. However, if you're not familiar with Linux, that slight edge will be against you because of administration headache.
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