I have written several times over the years about a project on Source Forge to do a Linux PLC. Originally a bunch of anti-Microsoft rebels, they completed an implementation that includes IEC 61131-3 programming. Originally Sixnet offered an RTU/PLC that would serve as a target for the Linux software. Now I just found out that Wago also offers a Linux PLC. So, if you want to run an alternative system, you have options.