We-ell,
"The Sea Devils" is sort of the follow-up to "The Silurians", and I'm pretty sure it's also the first instance of the phrase "reverse the polarity of the neutron flow", which makes it pretty neat. It also features Roger Delgado as the Master, whose performaces, I think, are absolutely unmissable for the dedicated classic Whovian. (I know you've already seen "Terror of the Autons", but really, there is no such thing as too much original-recipe Master. It's just not possible. In that vein,
"The Daemons" is a pretty good outing for him too.)
Speaking of "Autons", the story that comes just before it, called
"Inferno", features a really neat alternate-universe story within some stuff about drilling into the Earth's crust and people becoming monsters. The first Pertwee story,
"Spearhead from Space", isn't too bad either, and you get to see all the neat things that caused me to fall completely base-over-apex for Classic
Who. And I dunno if this is a popular opinion among Classic Whovians, but I really like the premise and ideas behind
"Carnival of Monsters".
"The Three Doctors", which also features Omega, is pretty awesome for its guest appearances (even though the First Doctor only appears on a little screen), and while I like the two Peladon stories, they're basically about intragalactic politics and Machiavellian intrigue, so YMMV. Oh, and I think the Third Doctor only has two Dalek stories, and both of them aren't bad, but really, Three shines brightest away from the Daleks.
You might also go with
"The Green Death" and
"The Time Monster" to see how Jo Grant leaves the TARDIS and Sarah-Jane Smith enters, respectively, and
"Planet of the Spiders" is pretty much unmissable because it features Three's regeneration into Four (which made me cry because dammit, I didn't want him to go
).
!
