I need a server, and I'm used to windows at home and in the office, but it seems that Unix / Linux is an option, but I don't really know what it is. I don't know which one to get, how do I choose? What kinds of questions do I need to ask my host (if applicable)? my system administrators? my programmers? is there anything else I should know?
Ask your programmers what language you need to be using, this is the most important part. Not all languages work on Unix and Windows.
Take the language information to your Host, and ask them what environment it's supported in. You, also, need to ask your host whether the Sever will be Managed or Unmanaged. Managed means if you have any server problems the Host will fix them for you, if you put in a ticket with support (my $dayjob). Unmanaged means you're on your own. In the Managed scenario, you will get some kind of web interface control panel, such as cPanel or Plesk.
If you're unmanaged, you should have actual employed system administrators, ask them what they want. Or you need to be able to be a system administrator yourself.
If both windows, and *nix turn out to be suitable for your needs, go with the cheaper of the 2, if they both cost the same, find out what the admins (including the ones at the host) know better, or which department (windows or *nix) has more admins.
The most important question to ask:
Do you have experience with Linux servers?
If the answer is NO across the board, then go with Windows server. In this case maintenance costs will outweigh licensing costs.