Yep, manually you have a few options but automated you only really have SEOSpyglass.
If you want to know how to use Blekko to scrape backlinks manually, check out my thread http://www.blackhatworld.com/blackhat-seo/black-hat-seo/377324-hot-how-check-backlinks-blekko-screw-yse.html
Can someone confirm if spyglass even works anymore?
I heard they are using YSE as well?
hum...
Cant believe SEOspyglass is down as well (i didnt even know they were using YSE).
What about Market Samurai? Do they use their own backlink database or YSE?
Thanks