The What code should you learn? infographic has a nice summary and history of different programming languages. At the end...it doesn't really matter all that much - for GIScience I would recommend Python, maybe JavaScript, and something like R or MATLAB.
Need convincing? Have a look at Pick Up Python!
Speaking of Python: Learn to be a Python Charmer compiles a bunch of great resources to get you started.
Here's another infographic: Which Programming Language Should I Learn First?
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