Does anyone have any suggestions of large open source projects with high quality code that would be good to study.
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Community Server is fairly substantial for an ASP.NET app and well written. It's sourcecode can be viewed online: http://code.communityserver.org/
Before writing the Stripes book, I read pretty much all of the source code for Stripes to learn it inside out. I was very impressed by the quality of the code at all levels: design, extensibility, interfaces/implementation decoupling, documentation...everything is top notch.
See the thread pointed by Alexander for C# projects. For Java, I'd recommend Spring Framework. It's a big, well managed project with good documentation and very clean (even if somewhat verbose) code.
SharpDevelop
In Java-land, Apache Mina and Stripes are two projects that come to mind. While I haven't actually hacked their source codes, I get a warm and fuzzy feeling that these frameworks are well built when I use them.
Scott Hanselman has been reviewing applications and their respective source code in a series "The Weekly Source Code". Pretty in depth and diverse stuff.