Executing Multiple Notebooks at Once

You can use several Mathematica kernels for this purpose.

Go to Evalution -> Kernel Configuration Options. In this menu you can add new kernels.

After in notebook, you can specify which kernel it must use by Evaluation -> Notebook's kernel.

Usually, I use two local Mathematica kernels. When default one is doing some number crunching, in other notebook, which I want to run interactively, I use the other (not busy) kernel.

For Mac users, you can use the command below to launch the second Mathematica instance. So you could run two Mathematica instances.Then you can open different notebooks in different Mathematica instances.

open -n /Applications/Mathematica.app