Who keeps Wordpress themes up to date? Or removes unused ones? The WP version updates are always to wp-admin and wp-includes. Themes live in wp-content. A colleague started getting browser alerts about malware on their sites, sporadically (not hosted at FQ by the way). Turns out this thing is called the TimThumb vulnerability and it installs a password grabber via uploading PHP as image files. It temporarily installs a whole shell emulator written in PHP. TimThumb has been blamed, rightly, and though its (freeware) developer has now updated the timthumb.php file, some theme places have stopped using the file completely.
Delete or update any timthumb.php files!
The malware looks for timthumb.php, even in themes you do not have active! Updating themes is not so easy, because you have to carve out previous customizations. So far Elegant Themes, a paid service, has been unwilling

to provide me with archived versions of their themes so I can do diffs without bugging my customer, "Do you have that zip file you downloaded five year ago?"
If you see any date changes to wp-admin.php, jquery*.js, l10n.js, or if upd.php appears, check out the WP forums for more info on TimThumb. The infected files will contain "CURL_OPT" (php) or "0x4de4" (js), and will have recent dates. So it's easy to find, but the next time could be worse.
The fact that WP themes contain PHP files, and that they are even editable from the admin interface, makes this vulnerability another reason to appreciate the wall FQ puts between shared hosting accounts,
PHP Secure_Mode.
Another good practice is to delete wp-admin and wp-includes completely when updating WP. It would not fix timthumb.php, but it could remove some if its previous damage. The sites were hosted with a host that has SimpleScripts, allowing one-click installs & updates of WP. Well, the one-click updates do not remove old cruft in those two directories! FQ does not offer one-click WP, but the FQ hosting environment does allow one-click updates from within WP to work (in contrast to some other hosts). I haven't checked whether WP's update code removes cruft.