Selecting Multiple Items
You can select a series of Docs by checking off one at the top, holding down Shift, and then selecting a bottom one. This will allow you to select a large amount of Docs for organizing into collections.
You can also select various Docs located in your list by using Ctrl or Cmd to select multiple items as well.
Dragging and Dropping
Don't forget that you can still drag and drag a series of files. Now that the checkboxes have returned, you're able to easily see what you're going to drag - and this is really useful for when you have a larger number of Docs that you want to organize.
You can still use the Actions menu item on the left hand side to do this as well.
Selecting Everything
One great way you can now select everything in a collection is by using the uppermost checkbox that is located right above all of your Docs. You can then tick off certain Docs to exclude by using your Ctrl or Cmd key.
Perhaps you never even knew that checkboxes mysteriously went missing for a while in Docs. Either way, these are some great ways to manage everything you have in stored in there.