The Dock is great for applications that you use very often, but it is not realistic to have every application in the Dock. Going to your applications folder just to launch one of those application that you use less often is also a pain. I thought the solution was to just drag the applications folder to the Dock and use it as a stack, but unlike in Tiger, icons in stacks are displayed too big to really be efficient with a huge number of files. The grid would just fill up my whole screen, making it a not very practical way of looking at it. What I really wanted was a way to pick the apps I wanted in the stack. I didn't want apps to appear both in the dock and in the stack. Dragging the apps out of the applications folder was not really an option either. The solution is however quite simple:
1. Create a new folder and put it wherever you want on your computer.
2. Open both the new folder and the applications folder in separate Finder windows, side by side.
3. Drag the applications you want in your stack to the new folder but while holding down "Option - Command". An arrow should appear when you are dragging it, meaning that you are not actually moving anything, just creating aliases.
4. Once you have aliases of all the applications you want, drag the new folder to your Dock, beside other stacks.
5. That's it, you can now use this stack to launch applications that are not used as often.
The folder:

The result: