My prefered file-manager (I use it everywhere: Gnome, IceWM...) is ROX Filer.
Unfortunately, whatever alternative you choose, I don't know how to setup Gnome to open your chosen file-manager to handle files by default.
Example: there's a dir for which you wish to have link on your Gnome panel. From eg. ROX, you drag'n'drop the dir to the panel. Alright, this makes a launcher of type "link" that points to the proper dir. So far, so good. But if you click on this link, Nautilus will open instead of ROX because Nautilus is still the default handler of objects of type "file"...
Share you results
Yves.