So, it depends, exactly in what you're looking for.
In case you're looking for loading speed, I think the best solution is keep them separated, it will allow the browser to load more than one js file asyncronusly.
But, if you need to have smartest code you should keep them in one single file, trying to reduce it more and more.
Remember that you should only think about this on your production code, absolutely is better to have different file working on them.
As you can see if you try the first approach you'll be more fast on page load. An example is a web application who need to load big amount of js files.
loading 3 file of 1MB will be always more fast that loading a single one of 3MB because they will start their loading in the same time.
Another approach is to load js files when your page requires them, but remember that in this case, if you have big js files, the client will see a lot of loadings during his surf on the website your working on.
Here you can read more about js file managment