It depends on the champion you play. From my experience against him, there are 3 types:
1. Champs with burst damage who harass him (without taking too much damage) and then turret dive to finish him before he kills them. Katarina, for example. It's very painful to play mid against a heimer, but it is possible to kill him with Kat and not loose your tower first. Ezreal would be another example I suppose.
2. Champs that shred his turrets whilst taking no or little damage in the process. Heimer will eventually run out of mana or at least is limited because he has to rebuild turrest all the time. Without turrets he can't farm very well. I think Mordekaiser is a good example for this category, he shouldn't have much trouble killing heimer as well at lvl 6. I think Karthus fits in here as well, though i can only guess since I don't play him.
3. Champs that can't counter him. As it is, not every champ is effective against any other. In case of Heimerdinger, perhaps the number of champions that can't counter him is a bit higher.
As to type 3, it's not necessarily OP that you can't counter Heimer with any champion.
I.e, a Kassadin mid will own many casters like Ryze or Veigar but is hard pressed against most DPS like Tristana or Tryndamere.
Against heimer, if you don't have a good counter, gank him. If 2 players focus him and dodge the grenade (not that hard) he is down in no time. You will need a good ganker since travelling across the map won't earn you exp or gold, and you need a lane mate that can handle a 1v2 situation (like heimer xD). A jungler that drops by for ganks also works very well.
Now someone will say that it is OP that you need a certain champ against him or have to gank him, but thats wrong. I.e., try laneing against a Mordekaiser in mid, that's also very, very painful for many champs, since he outfarms them and takes next to no damage with his shield. A pro Karthus can also be very difficult to face, unless you outrange him.