Personally I'd rate Season 4 as the best, John Lithgow and Michael C Hall were fantastic on screen together. Deb's breakdown over Lundy had me in tears as well.
Least favourite is probably 3.
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I have to agree, season 4 was the best, but the first season comes a close second, it set the whole Dexter story up, with his brother in that season.
That first season was pretty much perfect, as an introduction to the characters, and the story with Brian was so gripping.
The first season follows the first book quite closely, but after that the scriptwriters started branching out(I think mainly because some of the stuff in the books is so gruesome, you couldn't put it on TV for a mainstream audience).
I never read the books, I wish I had now.