ConfigurationCheckExecutor has the following code

       Configuration original = resource.getResourceConfiguration();
       if (!liveConfiguration.equals(original)) {
          log.info("New configuration version detected on resource: " + resource);
          this.configurationServerService.persistUpdatedResourceConfiguration(
            resource.getId(), liveConfiguration);
          resource.setResourceConfiguration(liveConfiguration);

(which runs in a tight loop for a long time, thus using a lot of CPU and blocking other work, but that is a different story;
2013-11-11 14:43:49,292 INFO  [ConfigurationManager.threadpool-1] (rhq.core.pc.configuration.ConfigurationCheckExecutor)- Configuration update check completed in 544077ms).

This assumes that we keep all resource configurations in memory. 
Such a configuration can use several kilobytes (for my current, already slightly tuned, heap, 7000 Configuration objects with ~64k PropertySimple take 12MB, with ~2100 resources, that is on average 5KB/resource) and with thousands of resources in memory that support configuration, this easily adds up to several Megabytes of heap.
As the configuration checking and also updating only happens infrequently, we could passivate those configurations to disk and read them back on demand, thus freeing a lot of heap.