Hacked by a Linkback request

I have tried to clean up a number of spam files on various sites since discovering that one of them was generating spam. As luck (and the alphabet) would have it I found a modified index file in my app-admin directory on the last site out of 13 on this server. The file was changed in Oct 2009, but nothing had happened until Dec 2009 when new files were written to the sites.
I checked that site for posts in that month to see if I had uploaded something to a post, that might be corrupted. There was nothing but text in the posts, but I did notice that I had accepted a linkback request from someone in Oct 2009.
When I clicked on the link to their site, it came up with a hacked message.
I have implemented as many of the recommendations from Esmi, as I could so far (just 24 hrs into cleaning this up) in reply to my security concerns and that is how I found this malicious code.
As always, many heartfelt thanks to one and all who do this support.
My question, since this appears to have been a long hidden hack, is there anything more specific to this type of attack that can be implemented? Or just continue on being vigilant and searching for intrusions?