I\'m developing an intranet application (C#) that uses some data (local to the web server) that we\'d like to keep private. This data is encrypted (AES) using a legacy data
Speaking in obfuscation terminology, what you are after is called constant hiding, i.e. a means by which you transform a constant into, say, a number of functions and calculations that are executed at runtime to re-materialize said constant.
This still falls within the domain of obfuscation, however, and is susceptible to either code extraction, where the attacker simply maps out the code relevant to this constant, and runs it in a separate application to retrieve the value; or dumping the application's memory at the right point in order to scan it for the desired value.
There is another, slightly more advanced method of hiding crypto keys in particular, called White-box cryptography, which employs key-less ciphers through essentially generating a cipher function from a given key, baking them together. As the name suggests, this method has been devised to be resilient even in a white-box attack scenario (the attacker has access to the bytecode and is able to inspect and manipulate the executable at runtime).
These are both quite advanced methods of achieving security through obscurity, and it might be worth considering alternative models which do not force you to do this in the first place.