I've used both from perl, and I would say, use Goo::Canvas for a few reasons. One, is that it has less dependencies, GnomeCanvas depends, as it name says, on some Gnome libraries, where as Goo::Canvas does not. A second difference is that the Cairo support of Goo::Canvas is superior to the Gnome::Canvas model. E.g. Goo::Canvas supports svg-like paths, that may be easier to use than the Bezier path of Gnome::Canvas. The difference isn't large though.
I also have a feeling that Goo::Canvas is still being maintained wheras the Gnome::Canvas stopped its support several years ago. I might be mistaken on this point though.
