>>How can I store a DB connection string with my C# project? I have different string determined by where I'm working at, so I'd like make it work around that.
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>The application's web.config file is the recommended location. I'm pretty sure you can encrypt the connection string (or is it the entire file?).

FWIW, you can encrypt specific sections. http://www.codeproject.com/KB/aspnet/webconfig.aspx has a VB example