Best free alternative is the new Bing Link Explorer
It can be argued that the original Yahoo site explorer was the best source for back links, it returned a comprehensive data set compared to Google's 'link:
Current worthy alternative is the Open Site Explorer however the free version limits it's search results and number of daily search
The potentially best new viable alternative is the just added Bing Link Explorer webmaster tool. The most important thing here to be aware of is that it lets you analyze inbound links for sites you are not verified for! Meaning you can analyze the competitor's back links.
However current data set appears to be limited, I believe this will only improve as the tool matures and so I will definitely be keeping my eye on this one.