In: Chemistry
There is a software especially designed for chemistry. Its name is "Chem draw 3D" or in some version there is also written as "Biochem 3D" or "Chem3D". If you want to buy it you can from "www.cambridgesoft.com" just go to link, search "Chem draw 3D" and buy it. You can even get pirated version in internet for free. But it does not show 3D orbitals.
Below is the Interface of Chem3D,
There are lots of 3D animation software but I prefer "blender" to draw molecules.You can find many video in you tube regarding the use of blender. But this is not just designed for chemistry so interface is not so simple...
I also heard about "Chem Tube 3D" but i don't know in detail...