Both are return the same value most of case but they have some deference.
System.AppDomain.CurrentDomain.BaseDirectory
Get the base directory that the assembly resolver uses to probe for assemblies
Security: for access to the information in the path itself, including if the path is in the form "file://" or \\UNC\dir or "c:\"
System.Web.HttpContext.Current.Server.MapPath
return the physical path of you application that correspond to the specified virtual path on the web server.
In Visual studio 2010 test projects, if you enable deployment option of Edit test settings, AppDomain.CurrentDomain.BaseDirectory points to the
TestResults\Out folder(not bin\debug)
. Although, default setting point to
bin\debug
folder.