I've been pretty happy with SpiderOak overall. I lucked out and got a coupon to get 'unlimited' space for relatively cheap, so I like that I can back up all of my machines without worrying about needing to pay more.

1000s of small files, or one rapidly changing file cause me problems as well. It's also annoying that each client has to decode new data whenever something is backed up on another machine. This causes my cpu to hit 100% on my laptop while my desktop is backing up a bunch of new files.