Translation:What are the benefits of this system?
The choice depends on context, but this appears to be a general question where there isn't a predetermined or restricted list of possibilities and almost anything could be defined as a benefit, and in that case what rather than which is the best option. It's bit like asking "Which is your name?" - that sounds really odd unless you were pointing at a list of names.
This short article covers more situations, including ones where both words could be used with little difference in meaning: http://www.bbc.co.uk/worldservice/learningenglish/grammar/learnit/learnitv175.shtml