Can you clarify what you mean by integrating with Nexus?
What are you trying to do, at a higher level? Do you want to just build a Maven project using RTC Build, use the Maven SCM plugin to checkout/checkin changes, or run tools to publish information to the bulid?

For the current state of our Maven support, please see https://jazz.net/wiki/bin/view/Main/BuildFAQ#MavenSupport

RTC itself doesn't provide any tools for managing Maven repositories.
You could try m2eclipse to ease working with Maven from with RTC. I know it has support for browsing/indexing Maven repositories. I'm not sure about publishing.

Here is the situation: "We have some dependencies in our project on JARs that are not available in the maven central repository.
We need our own repository so that when we run maven it will be able to pull down the necessary jar files. At my last job we used Nexus for our in house repository."

I think one solution might be to use a Maven plugin called Tycho:

Tycho is a set of Maven plugins and extensions for building Eclipse plugins and OSGi bundles with Maven. Eclipse plugins and OSGi bundles have their own metadata for expressing dependencies, source folder locations, etc. that are normally found in a Maven POM. Tycho uses native metadata for Eclipse plugins and OSGi bundles and uses the POM to configure and drive the build. Tycho supports bundles, fragments, features, update site projects and RCP applications. Tycho also knows how to run JUnit test plugins using OSGi runtime and there is also support for sharing build results using Maven artifact repositories.

Lately I have been playing around with installing RTC + M2Eclipse + Tycho. Tycho has a maven goal that will automatically generate pom files in each of your projects in eclipse.

Example command:
mvn org.sonatype.tycho:maven-tycho-plugin:generate-poms /
-DgroupId=org.dave.myapp /
-Dtycho.targetPlatform=${path-to-eclipse}

Once this is done you can simply run the normal maven goals such as:
mvn clean install /
-Dtycho.targetPlatform=${path-to-eclipse}

This also allows every eclipse project/plug-in to be packaged (into a .jar say) and put in your local Maven repository (.m2/repository/...) to be used by Maven elsewhere.

I suggest reading the 3 articles posted here for additional information:
http://mattiasholmqvist.se/2010/02/building-with-tycho-part-1-osgi-bundles/