It is the best STARTING PLACE to check anything. I do like that they put their references in their articles, something most sites don't bother with. They also encourage readers to investigate further.
They will admit they aren't 100% every time, and even if they can't prove or disprove something, they freely admit it.
So far, in nearly 20 years if using them, I've not found any discrepancies. Still, because most of what I've had dispute was political chain letters, I've had to use them as a starting point, and find other sources, but they point me in the right direction.
I think there are two reasons why they have a bad rep. The negativity comes from Conservatives, the further to the right, the more negative. It disputes what they consider God's natural order of the universe. It also debunks their chain letters. So what do they do? Even though they distrust the site, if they get an email that meets their world viewpoint, and it says "I already checked Snopes about this and it's true: see for yourself! (Snopes link)" but, if you follow the link, it disputes everything in the letter. Tell the sender that, and they get pissed.
In a nutshell, use them, but check their references. Other fact sites, aside from Politifact, actually use Snopes as a resource. Go figure.