I use Lightroom for Canon and PhaseOne files. You can create a custom export that will copy the selected files (for example all with 5 stars or the green flagged) to a different folder.
Then you can just open the selects in this folder with any RAW converter you wish. I'm using several different RAW convertors but want to have the workflow all in one tool. For that currently I guess Adobe Lightroom (watch out v2 is ins beta now and available in 64bit so it will come rather sooner than later) or Aperture are your best bests (although I haven't ever used Aperture as I work on PC's).
Best,
Boris