In .NET — nowhere. .NET Framework has nothing to do with breakpoints. A concrete set of breakpoints and their states is related to development process only and its persistence can be proprietary to development tools.
I just checked up my guess about where breakpoints are stored by Visual Studio. A simple experiment confirmed my guess: the breakpoints are attributed to the state of a solution (and not a project) and are stored in the .suo file. This file should not be considered as a part of source code. This is a temporary file used to persist solution state during development; it should not be published, put to the code base using Revision Control system, preserved when a solution is moved to a different location, etc. Doing so is a common mistake.
[EDIT]
What
is related to .NET Framework is the support of debugging in the .NET application using the class
System.Diagnostics.Debugger
,
http://msdn.microsoft.com/en-us/library/system.diagnostics.debugger.aspx[
^]. This is something different from the breakpoints you mean, but is important part of .NET functionality. I appreciate the post by Simon where he pointed it out.
—SA