Which java version to take for RTC SDK ?

If you check the system requirement for RTC, you will see which Java version is bundled. Is it what you are after?

Form example, here
https://jazz.net/library/article/811#mozTocId315994

You can find
IBM Java SDK 6.0 SR10 FP1 and future fix packs [Bundled]

Since future Java fix pack is always supported, you can obtain and install a particular version of Java and specify this version for RTC to use. In this case, you may not need to worry about the different Java version coming with different RTC clients.

Is this page kept up do date?

We are currently using 4.0.5 and are planning to jump to 4.0.6 asap.

That means that the 4.0.5 server is running under the mentioned Java 6 versions?

Actually, the system requirements page moved to here:
https://jazz.net/wiki/bin/view/Deployment/CLMSystemRequirements
You can check which java version is supported with 4.0.6:
https://jazz.net/wiki/bin/view/Deployment/CLMSystemRequirements#A9_Java_Runtime_Environment_Serv

I would suggest to use the Java Version shipped with the Eclipse client or the Server (Tomcat). We have seen issues with Oracle Java, especially 7.x. I always use the JDK shipped with the client/server and I have never seen any problems.