cmendla - 2:16 pm on May 29, 2013 (gmt 0)
Trying to prove your site is malware free is difficult. You can't prove a negative.
The process is a bit labor intensive. Suppose your are running a joomla based site.. Here is some of what you need to do. I realize you might not be running joomla, but this is illustrative.
1. Go through your public html structure folder by folder looking for anything odd such as htaccess files redirecting.
2. Look up and add extensions that are designed to protect against sql injection attacks and brute force password attackes
3. CHANGE YOUR WEB HOSTING CONTROL PANEL AND SITE PASSWORDS IMMEDIATELY. Make sure is is a strong password.
4. Look through your user list for anyone with admin privileges who shouldn't have them.
5. There are validators for Joomla that will check your core files to see if they have been tampered with.
6. In the case of Joomla, you need to update all of your core files and any vulnerable extensions.
7. Take a good look at your logs for any evidence of suspicious activity. IP Block any obvious bad guys. Keep looking at the logs.. That is tedious but you should be able to spot things that 'don't look right'
9 Monitorscout is right about google webmastertools. However, I have seen sites with malware where wmt did not report malware.
10. If you are running SQL, take a look through your database and see if there are tables there that don't belong. Be careful deleting anything.. Ie.. suppose you have a site selling widgets.. you go through your database tables and see an odd table. You browse that and find a whole boatload of credit card info.. Ooops.. probably someone is storing stolen credit card info on your site.
11. Always have regular backups of your site.. At the first sign of malware, you *Might* want to roll back to a backup.. Keep in mind that will cost in terms of content and user input being lost.
Hope this helps a bit.