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Hi happygirlftw (nice name!) While I don't have any direct experience using the "nocontent" tag, I can't see any reason why it should hurt you. This seems to be exactly what it was designed for. Adwords offers a similar type of tag for web publishers called section targeting. I've used it to great success and it doesn't have any effect on organic results. Finally, I'd be curious as to why Google couldn't identify the boilerplate content of your site on it's own. Google custom search uses different algorithms than regular search, but in this day and age we encourage most webmasters to reduce their boilerplate content, so this might warrant a closer look. Best of luck!

Orchard is a CMS that is open souce but funded by Microsoft. While not perfect for SEO, it produses a lot cleaner code then wordpress. It is ASP.NET MVC, I tried it out and was impressed, but i believe they still need a few more versions to iron out all the bugs, but then WordPress is full of bugs and its been around for a long time.