Yeah, I ran across malware once that only injected JS for visitors from certain referrers, such as Google search. I believe the intention was so that when someone would tell me, "Hey, you have a bunch of weird links on your site" I would go to it directly and not see a problem. IIRC the .htaccess had been modified.
What a mess. I hope running Chrome via EMET is enough to keep my machine safe.
I've noticed that hacks have gone up recently in my little part of cyberspace. Things like Cryptolocker are so profitable that its motivating a lot of talented guys to get into malware and hack servers. Usually servers running some unpatched CMS or module.