Actually there are still significant issues under Mono 2.6.3, I put in some workarounds to prevent these issues from completely breaking the site but the issues remain.
It seems that anywhere that we use the UpdatePanel, Mono does not seem to see the controls contained inside the UpdatePanel and can throw null reference exceptions when you refer to them in code in some cases.
The biggest error was happening inside our mojoRating.ascx.cs so I had to add conditional compilation to make this control not render under Mono, so content rating system does not currently work under Mono but this kept it from causing the yellow screen of death.
Also in other places the UpdatePanel doe snot seem to update the page. For example in the PageLayout.aspx page where you add a feature to the page, the feature does not show in the list unless you refresh the page.
There may also be additional anomalies as my testing has not been exhaustive.
I could really use some help in identifying these issues and reporting them to the Mono team because I am so busy it is difficult for me to find time to focus on Mono issues.