Earth's surface can gain heat through 4 ways I can think of (and this is just what I can think of and is likely wrong):
1) Geothermal brings more heat from core/mantle up. I don't think this is currently any larger than normal, nor do I imagine this varies much.
2) Oceans can give up heat they are storing and provide it on the surface. I don't know if El Nino is this, or if that just means "surface" ocean temperatures are up from whatever source.
3) Solar radiation (including infrared) can be higher than normal. I honestly have no idea if there's any significant variation in this, ever.
4) Earth can retain more heat that it was previously (global warming, be it man-made or not)
When they say the annual variation is usually hundredths of a degree, that sounds to me like 1-3 are generally non-factors, but that's all gut interpretation. Can someone with actual knowledge validate this?