I clicked around a little on his site. Most of his conspiracy theories appear to be political and he's clearly been mind-killed by politics.
As for evaluating "conspiracy theories", I recommend you start by reading this blog post by Eric Raymond, also this comment by Konkvistador if you haven't already seen it.
Sounds like you might not have read enough to see where his strengths and weaknesses are. Politics is his weakness and I mostly ignore that stuff, but I'm more interested in his paranormal stuff including the military-occult stuff, where he seems to have less of an ax to grind and sometimes presents a bunch of interesting source material without trying too hard to spin a story out of it. E.g. I like his report on Fatima, linked in my previous comment; what do you think of that one? (Though I suppose I should have told Multiheaded that Wells' political stuf...
I'm worried that LW doesn't have enough good contrarians and skeptics, people who disagree with us or like to find fault in every idea they see, but do so in a way that is often right and can change our minds when they are. I fear that when contrarians/skeptics join us but aren't "good enough", we tend to drive them away instead of improving them.
For example, I know a couple of people who occasionally had interesting ideas that were contrary to the local LW consensus, but were (or appeared to be) too confident in their ideas, both good and bad. Both people ended up being repeatedly downvoted and left our community a few months after they arrived. This must have happened more often than I have noticed (partly evidenced by the large number of comments/posts now marked as written by [deleted], sometimes with whole threads written entirely by deleted accounts). I feel that this is a waste that we should try to prevent (or at least think about how we might). So here are some ideas: