I love Stacks. I didn't use it for a month or so after upgrading but now I dig it. What I did was create a bunch of folders, each representing a group based on my workflow. So, Business, Graphics, Web, etc. In each of these folders I put an alias for common applications I use in that group and then dragged the folder into my dock.
Attached is a grab of my "Business" Stack, for illustrative purposes.