The trouble starts where Mono actually attempts to provide compatibility between Windows and other operating systems. A pure Mono application like Tomboy is unlikely to be harmed by this. The problematic part arises from the fact that Microsoft hasn't submitted all parts of the .Net stack to ECMA. So attempting actual compatibility can become dangerous. Microsoft doesn't exactly have a clean track record on the field of fair competition, so one has to wonder whether it is likely for Microsoft to use its patents to stop the Mono project when it becomes too successful.
Remember, in this context, that Microsoft has promised not to sue Novell and its customers for infringement with regard to Mono. According to Miguel de Icaza, this promise extends to Novell, its customers and its developers. When we read this the other way around, it does *not* extend to Mono users who are not affiliated to Novell. This scares me. You'll have to decide for yourself in howfar this scares you.
Now imagine Mono-based software is pushed into the popular distributions on a larger scale. It would be possible to replace a pretty large amount of readily available programs with Mono-based counterparts. Think Banshee, Beagle, Gnome Do, F-Spot, Tomboy, Muine, just to name a few.
And now image Microsoft legally pulling the plug on (parts of) the Mono project, taking the whole Mono eco-system with it, just when people got used to Mono-based programs. Ouch.
I'm not saying that that problem would be insurmountable. Au contraire: it'll probably create a huge drive in creating non-Mono alternatives. But it will hurt us. And it is unnecessary: we have C, C++, Java, and Python-programs right now.
Personally, I don't really like the whole Mono thing. I think the whole interoperability business is bogus. I think we do not need Mono. In fact, I think the whole Mono project is redundant and that it should be looked upon with great suspicion. I may be overstating it a bit, but having been in this business for quite some time, I know that old dogs never learn new tricks. To quote admiral Ackbar: "It's a trap!"
Let's not put any more Mono-software in Gnome. And yes, let's support initiatives like gnote that provide alternatives to already established Mono-programs.
Anyway, if you want to rid you Fedora box of Mono, this aught to do it:
# rpm -e mono-web monodoc mono-addins mono-winforms mono-data-sqlite mono-data mono-extras f-spot tomboy mono-core gnome-sharp gnome-desktop-sharp gtk-sharp2 ndesk-dbus ndesk-dbus-glib gtk-sharp2-devel
Just install gnote as a Tomboy replacement, move .tomboy to .gnote and you're done.
UPDATE: It seems the guys at Fedora are on the same track and are pondering the replacement of Tomboy with gnote. And personally, I love them for it.