If you have Fedora Core 6 you are using Tomboy 0.4.1 because that is the latest version that Gnome 2.16 comes with. To me this is a nonsense and I didn't see any libraries that prevent tomboy to be updated to a newer version.
I tried compiling tomboy 0.6.3 (latest stable version) and 0.7.1 (latest unstable version) from source. I added missing dependencies that ./configure complained about (yum -y install libgnomeprint22-devel libgnomeprintui22-devel gtk-sharp-2.0-devel) but I still got some missing dependencies I couldn't resolve (gnome-sharp-2.0 and gconf-sharp-2.0).
After posting to fedora-devel mailing list I got a great suggestion - to install it from development repository.
That worked out great! And as I suspected there are no other dependencies, it is a clean update.
Just issue this command, and you are off:
yum update tomboy --enablerepo=development