<p>Is there a way to select designtime packages on a project bases?</p>

<p>Packages are very useful in large project to keep the build time acceptable, but they are a real pita in those large projects too. When one developer adds a new package, it breaks to build for all other until they install the new package on their machine. And then there is versioning of the packages ...</p>

<p>So has anyone a proper solution for this? (it has been bothering me for years now)</p>

This is not easy too do.  You can do it though, with the use of a custom registry hack, and a specific bds shortcut per configuration you are interested in:
To use, just create a new shortcut and
  modify the command line to pass e.g.
  -rMyAlternateBDSReg. Then after launching that once, the reg entry is
  created and they can configure that
  alternate registry all they want,
  deleting packages, etc, without
  worrying about messing up the default
  install.
From
codegear
If you set up a configuration for each project, you can then start the appropriate shortcut for the given project.  It's not automatic, but it is better than having everything there all the time.
A nice side effect is that the load times will be improved.