Odd, in all the years that I have used in linux I have never ran across such an issue (granted I gave up on using evolution years ago). Even KDE3 apps to KDE4 apps went smooth. I don't use gnome so perhaps ithe breaking of apps is a gnome feature. I even have one system that has had the same /home directory dating back to SuSE 8 and has been upgraded all the way to 11.1 with no major issues at all.
Over the past year I've gone from Ubuntu with gnome, to OpenBSD with Gnome, to Gentoo with XFCE, Debain testing/sid with Gnome, and back to Ubuntu again with GNOME with the same /home partition and had not one issue (well one with uid's not matching up but a chown -R fixed that).