I like Sub Heatran, made popular by Wolfey. I find that some SpDef heavy fighting types such as Hariyama and Conkeldurr make good counters. These two also don't mind being burnt. Another uncommon counter is Gyarados. It walls everything that Heatran can get, except maybe HP Electric. Also, Latios is a good counter without HP Ice. Most dragons such as Hydreigon, Salamence and Garchomp can shrug off attacks. Politoed brings eternal rain, dampening its fire attacks and usually runs decent special bulk or can nail it with a water move. Jellicent also walls Heatran to oblivion. Swampert can hit it with a super effective STAB move and resists Heatran's moves. Most bulky waters counter Heatran. I think Heatran appreciates a FWG core. The perfect partner of it is one of my favorites, Virizion! They synergize perfectly, resisting all of eachother's weaknesses. Rotom-W also makes a good teammate, resisting most types. These above 3 are a fantastic starting point for a team based around Heatran. It also enjoys Psychic types like cress and latios, taking out fighting types and resisting EQ. All of my sets have Heat Wave and Earth Power, two good offensive moves on Heatran. protect is usually there, and the last slot is a toss-up between HP Ice and Sub.
Happy to give VGC team rates! PM me anytime and I'll rate as soon as I can.
VGC 2013 San Jose: 2nd place Seniors Division