You can start with Google's Safe Browsing Diagnostics: http://www.google.com/safebrowsing/diagnos...www.example.com (replace www.example.com with your own site address). It will show whether Google found anything suspicious on your site.
Then you can analyze HTML/script code of your files on server. They should not contain anything that you didn't put there.
Then scan your server for any suspicious/new files and directories.
Then look through web server configuration. There could be unwanted redirects and error pages.
You might also want to take a look at my online tool called Unmask Parasites http://www.UnmaskParasites.com . It analyzes HTTP response and HTML code of web pages and highlights suspicious code (links, scripts, iframes and redirects). Google's Safe Browsing information is also included in Unmask Parasites results. Note, that the tool is still in beta and may not detect every security problem.