We have several products which have a lot of shared code and which must be maintained several versions back.
To handle this we use a lot of Eclipse projects, some contai
I'm not completely sure I understand the problem, but it sounds like the root issue is that you have many projects, some of which are dependent on others. Some of the projects that are closer to the "leaf" of the dependency tree need to be able to use "stable" (or previously "released") versions of the more "core" projects.
I solve exactly this problem using Hudson, ant, and ivy. I follow a pattern demonstrated by Clark in Pragmatic Project Automation (he doesn't demonstrate the dependency problems and solutions, and he uses CruiseControl rather than hudson.)
I have a hand-written ant build file (we call it "cc-build.xml", because of our CruiseControl roots.) This file is responsible for refreshing the working space for the project from the CM repository and labeling the contents for future reference. It then hands off control to another hand-written ant build file (build.xml) that is provided by each project's developers. This project is responsible for the traditional build steps (compile, packaging, etc.) It is required to spit out the installable artifacts, unit test reports, etc, to the Hudson artifacts directory. It is my experience that automatically generated build files (by Eclipse or other similar IDE's) will never get close to getting this sufficiently robust for use in a CI scenario.
Additionally, it uses ivy to resolve its own dependencies. Ivy supports precisely-specified dependency versions (e.g. "use version 1.1") and it supports "fuzzy versions" (e.g. "use version 1.1+" or "use the latest version in integration status.") Our projects typically start out specifying a very "fuzzy" version for internal projects under ongoing development, and as they get close to a release point, they "freeze" the dependency version so that stuff stops moving underneath them.
The non-leaf projects (projects that are dependents for other projects) also use ivy to publish their artifacts to our internal ivy repository. That repository keeps all past builds of the dependents, so that any project can always depend on any other previous version.
Lastly, each project in Hudson is configured to have a build trigger that causes a rebuild when any of its dependent projects successfully build. This causes them to get built again with the (possibly) new ivy dependent version.
It is worth noting that once you get this up and running, consistent automated "labeling" or "tagging" of an automated build's inputs is going to be critical for you - otherwise troubleshooting post-build problems is going to result in having to untangle a hornet's nest to find the original source.
Getting all of this setup for our environment took quite a bit of effort (primarily in setting up the ivy repository and ant build files,) but it has paid for itself many times over in saved headaches in manually managing the dependencies and decreased troubleshooting effort.