I removed the offending code from my Wordpress theme when I found it (and yep, it was some BASE64-encoded nasty that was doing it) but I found that even then, whoever it was managed to put the code back in afterwards.
It might not be a WP site, and might only affect one of your sites, but I'd be a little concerned about how they did it in the first place, or else simply taking the offending code out might not stop them from being able to put it back again. With me, I had to completely remove the theme, and the database amendments, and use something else.
Just some food for thought.
