I am a happy user of Fedora but most SCADA systems I know use CentOS. I am going to provide a SCADA solution in Linux. Should I convert to CentOS or stay with my friend Fedora?
Short Version: If you expect the system to be in use longer than 1 year, use Centos 6.
Long Version: The question for any application pretty much boils down to how long you want to run the system without major upheaval. Keep in mind that these types of concerns tend to end up being much longer than the temporary period initially expected.
(Note: I am using Red Hat Enterprise Linux (RHEL) and Centos interchangeably as they are binary compatible and Centos is typically a free substitute used in place of RHEL)
The Fedora Project actively provides updates for its two most recent releases (as of this writing, Fedora 14 and 15). You have the most recent set of packages, but you are on your own once version N+2 is released.(per Fedora Wiki)
Red Hat Enterprise Linux and Centos have a support Regular Support Life Cycle of 7 years and Extended Life Cycle of 10 years (per Wikipedia)
Prior to the release of Centos 6, there was a rather significant tradeoff to be considered between it and Fedora. RHEL5 was built on Fedora 6 which was released in 2006. Many of the packages were starting to show their age and people wanted to use a more recent package set for their applications (e.g. The latest versions of Mediawiki use a more recent version of PHP than that shipped with RHEL5). The release of Centos 6 changes all of this since it is based on the much more recent Fedora 12 with a lot of Fedora 13&14 changes backported.
Since you're choosing right now, there is very little reason not to target Centos 6 unless you really, really need a more current version of a package (thing long and hard about this). You will get both a very current package set and 10 years of updates.
Fedora has short release and support cycles. You typically have to upgrade to newer versions of the OS rather quickly to continue receiving support. When you're setting up a production server, you want to know for sure that you are going to be able to receive bug fixes and security patches for a long time. The CentOS support cycle is the same as RHEL, which I believe is ten years.
This advice is good for any server operating system. You want to know that when you set something up, it's sustainable for the foreseeable future.
CentOS is based on RedHat Enterprise Linux (Hint: Enterprise)
RHEL is hugely popular in larger companies, particualy in the financial sector. CentOS is built from the same packages as RedHat but without the support (or cost). Generally CentOS runs ~6 months behind RedHat with core updates etc.
Depending on your goal, there are advantages to both systems; CentOS/RHEL default repositories only include builds of software tried and tested to be secure, they never (or very rarely) include untested or beta packages. If you use RedHat security updates to software will normally be avaliable in the repositories within a month of being avaliable, sometimes within days for critical security issues. However CentOS again tails these updates by sometimes up to 6 months.
Fedora has the advantage of having much more up to date software. For example RedHat/CentOS 6 (The lates version) are based, AFIK, on Fedora 9. Fedora has more recent versions of most software avaliable in it's repos, as well as having, arguably, a larger 'user' community.
From what I understand theres not a huge amount of difference between the two, I use CentOS myself. I generally prefer to stay with what the industry is doing as far as applications like yours go. Theres no reason to reinvent the wheel, if its already running elsewhere on CentOS then you know you've got a lot less work to get it up and running. Just my 2 Cent(O)s.