While I'm not entirely sure if they're my "top three", here are three bands that I like a lot, that just happen to fall into the prog rock category in most cases. I think they're all worth a listen anyway. If you're already familiar with them, then... yeah?
The Genesis stuff from before Duke (or some would would say ...And Then There Were Three..., it's a thorny issue amongst the fans) is definitely very progressive and worth listening to. A lot of the weird element is provided by Peter Gabriel, with his lyrics and, if you're watching something live from the era, stage drama. I'd probably recommend Selling England By The Pound. The opening track, Dancing With The Moonlit Knight, is one of my favourites.
Emerson, Lake and Palmer are good choices in the progressive department too. Karn Evil 9 might be around half an hour long (and that's probably quite short if you're talking prog rock) with a mixture of different sequences but it's still great. Their version of Fanfare For The Common Man is good too. You've got to love that organ sound.
Finally, I've been getting into this album by Camel. I'm not sure how well known they are, but some of the stuff on there is great. It's good music to leave on while you're reading or something... but then again, quite a lot of progressive rock is like that. If you look into this one, I recommend Rhayader. Flutes are great, is all I can say.
Special fourth suggestion that I couldn't resist: Jethro Tull. Check out Heavy Horses.
