Any assassin. Though they will probably never lane, they can just come kill you whenever they feel like it.

Nasus walks all over Heimer once he gets a couple items. I've had problems dealing with Promote Heimers early game (like, level 4 early) but they can't do anything but die after Triforce.

An aggressive Volibear will eat your face early game.

just destroy him with maokai

I don't feel heimer is really that strong of a lane. Like harmar said, you can freeze your lane outside your turret with Maokai indefinitely and force the Heimer to overextend (and if someone ganks, you usually get the kill because Mao has so much CC).

Heimer is a pretty horrendous dualist, so if you can just pick a champ that jumps in his face, you will likely kill him.

What Heimer does best is ratchet up the pressure, building up a creep wave, slowly forcing it closer and closer to the enemy tower by moving his turrets forward, before dumping a mass of creeps on the enemy point to neutralise it. He isn't great at killing enemy champions, but he controls the lane like a boss.

This works best against people who cannot push. Champions like Maokai or Cassiopeia can destroy an infinitely large creep wave with a couple of spells. A single-target champion will have a hard time dealing with this creep pressure.

It also works best against enemies who can't kill your turrets. Any ranged AD champion with more than 500 range can kill your turrets without taking more than a couple of turret counterattacks, if they're behaving intelligently. (If you just run up to a turret, with no creep wave to steal attention and protect yourself, you will take a bunch of damage from it.) Most mages can take them out fairly easily too.

The best counters to Heimer are any champions who can push as well as he can. Because Heimer can only push, he's not a nuker, he doesn't really have any other strengths, if you nullify that strength, his lane becomes a liability.

Poor Heimer. He's one of my favorite champs but there are just flat out better choices out there both in Dominion and in SR. I hope he gets his rework soon (But I swear if they make his turrets a temporary emplacement I'm shelving him forever).

I play Cassiopeia and yes, she counters Heimer easily. I just Aoe+Q+E his turrets and they die. Then i can harass him by Juking his blind bomb then maybe taking some missile dmg but thats it..while heimer will be taking dmg from my AOE +Q+E until he puts more turrets down..then i just kill his turrets again and repeat.. easy

ap yi counters heimer.

yorick with manamune, spirit visage, Trinity force, saguine blade, and some MR from either odyns or FoN murders heim bot.
You 1 shot his turrets using omen of war and just heal up from his harass which barely does damage.

At that point heim gets pushed back to his turret and can only rely on ganks to kill yorick. At least that's how i dominated a heimer as yorick.

Pretty much everyone... specially if your assasins are doing their job, theres nothing heimer can do against ganks.

He used to get banned because ganks were not popular back then and thats why he still gets banned in basement elo where bot is the single player lane... I once had someone dodge because we didnt ban heimer (1.7kish elo, he was 1.2k)