Hunter S. Thompson is a personal hero of mine. I always thought it was odd he killed himself until recently where my chronic pain has gotten to a point that I don't know how long I can live with it in the years to come. That's what happened to Thompson. He had hip surgery, and constant pain from that. It got to a point that even with copious amounts of drugs he couldn't deal with the pain anymore.

So really, it was euthanasia. If I can hold out to 67 I'll be damned proud of myself.

I think the biggest factor against a conspiracy is that Johnny Depp got really close to Hunter while filming Fear and Loathing -- in fact, Depp has incorporated elements of Thompson's character from that movie into his own persona. He did the whole launch the ashes out of the cannon $21 million dollar funeral. If there was a hint of impropriety in Thompson's death I can't imagine Depp not pursuing that with his then sizable fortune.

edit: I wanted to add that his paranoid remarks may have been driven by "the fear," a state of nervousness and paranoia you get when coming out of a drug or alcohol binge. Afaik he coined the term.