For working with packing cubes, I recommend the Eagle Creek No Matter What duffels. I have the small and medium. Why I like them is their base is 12" wide. So even in the small, which has a 12" x 18" base, I can fit their 18" packing folder. I use the 18" packing folder for dress shirts. I put it in the duffel first, then stack in cubes, shoes, etc. Of course, If I am not bringing dress shirts and don't use the packing folder, the cubes still fit very nicely. The duffels are light, tough, and if not jammed completely full, fit easily in the CRJ overhead. The medium not jammed full will easily carry a week's worth of clothes.
The only drawback is because of the wide base, especially when using a packing folder that is fairly rigid in the bottom, the shape can be a bit awkward. My preference if I am going to be doing a lot of walking with my bag is to use a more vertical format (like the Red Oxx Air Boss). But when I'm not going to be doing a lot of waking with my bag, the duffel is my choice just because it is so easy to load and unload.