I assume this has been covered before but my quick search didn't result in anything useful.  For my spring break, I am hoping to organize my sets.  Right now they are just randomly put on shelves.  I have an open shelf, I get a new set, that set goes on that open shelf.  So I was wondering what is the best way to organize sets?  Do most go by theme?  Box size?  I want to basically get everything organized and more streamlined.  

I think you might get varying opinions on this. Basically, come up with a logic system that makes sense to you and then shoot for that. I go by theme, but depending on the size of the theme (star wars has a lot) I'll subdivide by size a bit as well to maximize shelf volume. And just remember, probably common knowledge but whenever possible, stack them like books on their spine, not on top of one another!