I don’t think submitting to Free SEO friendly directories can cause harm your website. 
Anyway you can visit the following websites for free SEO friendly directory list:
http://www.directorycritic.com/free-directory-list.html
http://info.vilesilencer.com/
http://www.seocompany.ca/directory/web-directories.html
If you wish I can submit your website to 3000 Free SEO friendly web directories.
Cheers,
SM