CICS Transaction Server, sometimes known as CTS and sometimes just called CICS, added support for WS-AtomicTransaction , as of November 2005. There's a tutorial for setting this up, on the IBM website. Essentially CICS TS can act as a provider or consumer of web services.
If you have questions on how this stuff works, I suggest the CICS listserv.
As far as interop goes, I would guess the basic stuff, theWSDL and SOAP, just plain works, when connecting CTS3.1 to .NET 2.0, or CTS3.1 to WCF 1.0. I am not sure on the version of the WS-AT spec IBM have implemented (you know it went through several iterations) and I do not have a CICS TS 3.1 region sitting around, ready to test this out on. . . . So I cannot say for certain that the WS-AT provided in WCF will interoperate with the WS-AT provided in IBM's CTS 3.1. I will check on this. if anyone has information on this in practice, I would love to hear it.
[Addendum - Andy Milligan points out that you can get WS-AT interop to CICS Transaction Server, via WCF and its integration with HIS2004. Two things: first, Nice! I love it when things are easy. Second: Whoops! I should have mentioned this. I like this option because it eliminates the need to upgrade host software, which is always expensive and tricky. It also eliminates the question of whether the WS-AT on CTS 3.1 is the same version as the WS-AT on WCF, and it eliminates the need to spend $5885 per user on the Websphere developer tool. Check out Andy's post for more on how this approach works. ]