Good thread! Tough to pick some of these but here goes:
RHINO---ASM # 617, 625--Joe Kelly's emotional two-parter just narrowly edges out "Flowers for Rhino" though I recommend reading both if you haven't.
GREEN GOBLIN--Nothing can top ASM #39-40 for me.
VULTURE--ASM #240-241; Roger Stern wrote the best Vulture, hands down. You can throw in his origin story from ASM #224 to make this complete.
KRAVEN---Kraven's Last Hunt....duh
DOC OCK--Probably the toughest to pick on this list. ASM #698-700 is certainly a contender but then again an argument could be made for ASM #88-90 which has, IMHO, the best illustrated Ock/Spidey fight scenes ever.
CHAMELEON---Another tough one! Web #51-52 is very underrated but JMD's arc in PP:SSM #242-245 is pretty great also. Throw in Mark Waid's "Red Headed Stranger" from ASM #601-603 for a tough 3-way race.
MYSTERIO---Nostalgia wins out for me here; gotta go with ASM #66-67 in large part for JR SR's awesome covers and interiors!
VENOM---Lots will pick his debut but I disagree; gotta go with his even better return story from ASM #315-317.
ELECTRO--JMD's "Light The Night" from Spider-Man #38-40. No contest.
SCORPION---His early Ditko appearances were by far his best and when he was a legitimate threat; his second appearance from ASM #29 is his shining moment.
HOBGOBLIN--I could cheat and just say every Stern story from his debut in ASM #238 straight through ASM #251---and so I will.
SANDMAN---Another villain who peaked during the Ditko days; will go with ASM #18-19, a great arc that I recently reread (again) and it gets better every time!
LIZARD---ASM #76-77; yes, "Shed" was a daring and well-told story but I gotta go old-school here.
KINGPIN---I really, really love "Back In Black" from ASM #539-543 if for no other reason than the beatdown that Pete gives old Willie! That aside, I guess his debut from ASM #50-52 is pretty great.
Those are most of the classic rogues that I can think of off the top of my head; again, great idea for a thread!