Bolt is certainly the first card that comes to mind, a few others off the top of my head:
Phyrexian Metamorph: best used to copy your own lodestone, though still has utility for copying generic spheres or against Oath...a deck that may or may not decline if aggro shops turns to more control shops.
Phyrexian Legionnaire: Cool because you could play it even if you are not on white, though the presence of triskelion in shops decks may have kept people from leveraging it to its full advantage...it came down un-taxed through a thorn AND a lodestone, and effectively acted like a 2 mana/2 life moat until you could get back ahead on mana/answers.
Pulverize: Am I really still setting myself back two lands if I am no longer consistently staring down 5 damage plus whatever else? This one is a toss up to me...if you are so far behind already that a well timed EOT hurkyls cant pull you ahead then you may have already lost.
Magus of the Unseen - What are you stealing now?
Some shop hate cards that may be "better" now:
Kohlagns Command - its CMC was the one thing that really held this card back, and with 3 Sphere slots up in the air it may be way more playable now...also a solid card vs Storm if you get a turn and can hit their hand and their artifact mana
Artifact mutation - its cost always held it back, and although Lodestone would be the tastiest target, EOT kill your sphere get 2 guys fits into the lateral strategy prevalent in the format today.
Radkos Charm- Double utility as Artifact and Graveyard hate, same Casting Cost issues as the cards above. I have been told by my dredge friends that this card is crushing and they seldom see it coming.
Rack and Ruin - This card used to be everywhere then suddenly 3 CMC became unrealistic...Would love to see this make a comeback
I agree pretty much with the top 4 cards, specially metamorph. Golem was often the chosen card to copy, now it's not possible anymore.
Also slash panter gets worse. The 4 damage was specially relevant when you could add another 5 each turn.
Moxen get a bit worse probably, but got MUCH better when chalice got restricted.
batterskull gets worse. it it a great card to bring in front of a golem, not so good against some 5/5 or 6/6
dismember is going to see less play. It was a 1 mana removal, specially useful in the mirror
vault+key was a great wincon under lodestone. now if null rod increases, vault gets worse
I expect to see more :
serenity: previously serenity was great, but that extra turn could cost the match, not to mention that it costed a good amount of mana at sorcery speed. with a slower clock, it should be better
null rod, which does some nice mana denial. Or maybe karn, but rod seems better.
welder: there are lots of people wanting 5c stax to come back
creature decks. I was playing merfolks + faeries when golem came out. I traded good results for utterly loses against golem
thought knot seer could see play. While it can not be paid with mws mana, no golem means that it does not cost more. 4/4 replaces the body and the effect is awesome.