Looking at netstat and ps can show you if you have rogue processes running on your box sometimes. There are lots of online articles about redirects or spambots with base64 code in them. Basically, what I do is grep through all of the domain files on the server and look for that string, obfuscated or not.
Code:
BADSTRING="e[^a-z]*v[^a-z]*a[^a-z]*l[^a-z]*b[^a-z]*a[^a-z]*s[^a-z]*e[^a-z]*6[^a-z]*4[^a-z]*_[^a-z]*d[^a-z]*e[^a-z]*c[^a-z]*o[^a-z]*d[^a-z]*e"
find /path/to/files -type f -exec egrep -l $BADSTRING '{}' +
TBH, I don't remember why I used egrep there rather than grep - I might have been searching for more than one string at one point, but whatever. On the plus side, I've found this (stuck in a larger script that emails me after checking the files once a day) quite useful. On the minus side, if you run this on your live server it will drive your load way up. This works best if your files are on a filer, or if you do nightly backups (unzipped) and can search the backups rather than the live files.