You left out my usual answer -- "the first half of season three and second half of season 4!"

Can't imagine how you came to overlook that option
I loved the beginning of S3, all the way up to the ARRRRGH, which sucked. IASWAA was okay, but not great. The NK arc started out interestingly but went downhill, IMO. And at the beginning of S4, they didn't seem to have any idea of how to write L&C as a married couple -- they had a honeymoon in Brutal Youth but then went straight to "old married couple" -- in love and comfortable, sure, but no steam. However, once they got that straightened out... I thought the late middle of S4 was fabulous, starting around Lethal Weapon. The John Doe eps were terrific, I thought the Lex Files was very well-done (they actually had *gasp* continuity! between episodes! and they kept making it more interesting). AKA Superman is probably the funniest episode ever <g> and even there, it's got a sweet b-plot. IGYUMS was a fabulous premise ruined by lousy acting from the guest star. Toy Story and Family Hour were just incredibly bad.
On this poll, I voted for S3, but it was close.
S1 -- emotional torture for L&C, and it's all "apart angst"
S2 -- dry as dust at the beginning, frustrating as hell toward the end
S3 -- started out great, then went down the toilet
S4 -- took a while to find itself
And as others have said, there were wonderful moments in every season -- in darned near every ep, there were a few seconds of greatness shining through
Actually, my favorite season may be
Season 6 
but then, I may be biased.
PJ