In early 2012, I had over a dozen sites across three accounts get hit with the same attack. As far as I can tell it was an exploit in the timthumb.php script, commonly found in WordPress themes.
While shocking and initially stressful, it became both a transforming experience as well as an educating opportunity; transforming because it finally pushed me to change my blog theme and do some much-needed house-cleaning of my server space; and educating because I learned a lot about both the security holes that were existing on the server, about better ways to use Git for faux-backups, and about some other under-the-hood security issues.
These people have linked back here, having had similar experiences: