I too organize by containers and typically have 5-6 I select from depending on what I feel like sewing. It helps me from getting projects mixed, especially the scrappys.
I do keep track of what I'm working on via Pinterest. I have 3 boards from my stuff: one is My Quilts for finished projects, one is Quilts in Progress so I can see what projects are incomplete and what needs to be done next, and one is Quilts on Deck for those I'm considering next. I also have a basket on my sewing table with patterns that have caught my eye and I want to sew.
Keeping a list on paper didn't work for me. Now, if I was sewing for others, I'd probably make something more formal.