As Ale said, it is a neuter definite article referring to any thing ( the third person in its neutral form) so it refers to things or concepts. So, if you say:
"lo que pasa es que..." you are saying "what happen is...
"lo que me está molestando es..." you'll say "what is bothering me, is that...
"lo que dije es..." = "What i said is..."
So as you can see, is not that hard, just needs a little practice!