This is still broken with gvfs. I can confirm it on Intrepid with the new ~/Private directory. Anything you trash under ~/Private is properly put into ~/Private/.Trash-$UID, but it does not show up in Nautilus's trash. This bug may be in the gvfs package rather than nautilus, but since I'm seeing it in Nautilus, let's start there.
This is still broken with gvfs. I can confirm it on Intrepid with the new ~/Private directory. Anything you trash under ~/Private is properly put into ~/Private/ .Trash- $UID, but it does not show up in Nautilus's trash. This bug may be in the gvfs package rather than nautilus, but since I'm seeing it in Nautilus, let's start there.