These are list of the ways websites can link or refer your site apart from direct hrefs that may not be found by using usual link commands, but can be found by SE’s like Google. This can also effect in your SE rankings to some extent.

# another site links to your graphics ( img src=http://www.searchengineworld.com/gfx/logo.png )
# a site links to your javascript files
# a site links to your css files?
# rss feeds and other xml feeds that people can link to without notice or referrals necc being generated.
# links in email that some se’s can read (yahoo mail, hotmail, Gmail)
# links marked with noindex
# links marked with nofollow
# raw urls within javascript or js comments
# raw urls within css or in css comments
# urls within meta data of graphics and video files.
# urls within html comments.
# urls within the head section, meta data of a html page, or alternate html entities (alt, name, id, etc).
# links or pages that maybe surfed while visitor has page rank engaged on the toolbar.
# the target of a constructed, obfuscated, or encrypted js url (hidden until executed)
# links behind pay walls that Google can spider via webmaster tools
# Domains that have been 301?d with links.
# Links in Flash movies (games, quizzes, etc).
# non href’ed url’s. (raw url on page http://www.techcrunch.com)
# Links in any documents other than web pages e.g. .doc, .pdf, .txt, etc.
# blocking a page in robots.txt should make it blocked from bots, but they still spider it.
# Domain registrations/Whois and DNS data
# Links in form data.
# Links in other Google produced software (gadgets, widgets)
# NonTraditional pages (irc, twitter, UseNet, Yahoo, or Google Groups.
# Google Adwords.