Throughout the years I've collected thousands of papers, many still unread, but my 'must read' ('must skim' mostly) folder currently houses several hundred of them and I can't imagine how much time I would've wasted by manually renaming using the template {Author} - {Year} - {Title}.
Mendeley is free, but a paid alternative is Papers (http://www.papersapp.com/), which used to be Mac-only and the reason I ended up discovering and using Mendeley. Haven't personally tried it, but heard very good things about it.
My paper reading selection process consists in reading the abstract and the conclusion. Quite a few papers have disappointing conclusions despite attention-grabbing titles. If all is sound and promising, I keep it and depending on other factors, I decide when to read it in its entirety and/or where to store it for later use.