For me, Kyuss invented stoner rock (in terms of what I consider stoner rock anyway), and are still the best. Also, most projects from their members, eg. QOTSA, Slo Burn and Unida (though the latter is not really stoner) is all worth a look. Fu Manchu, Nebula, Monster Magnet, The Atomic Bitchwax and Dozer are also personal favourites.
Further to that, I enjoy the transition from stoner rock through metal towords Doom, eg. Orange Goblin, Down and the mighty Spiritual Beggars. I also agree with plaguewilder that, no matter what catagory Clutch are, they are fucking awesome (Really looking forward to seeing them twice between the 7th and the 11th).
Oh, and I do find stoner rock sounds better when you're stoned. Music made by stoned people, for stoned people (not that you HAVE to smoke pot, thats just my view). Then again, I enjoy doing most things more when I'm high, so, as with most things, I guess it's down to personal preference.