I like boxes. When SMing was my bread and butter, I spent a fair bit of money on boxes.
I tape my props table into squares with lables for individual props, I have a whole bunch of palstic boxes with lids that I stack under the props table (for the props where there are lots of the same thing or for props that all go in the same place when setting a scene, ie for dressing a beauro) and I put a lable on the top with the contents of the box.
As far as organisation goes - large items at the back, small items at the front, organised in columns based on the scene.
If there is a really prop-intesive show, I have some large plastic boxes on wheels, and I will separate the props into 'sections' (usually acts), draw up a table for each section on plastic tablecloth (the cheap white stuff that comes on rolls that you cut to length) and an entire section goes into a box. The ASM for each side basically collects all props, when they are done, they go into the box for that section, when the table is clear, the ASM folds up the cloth, puts it in the box and lays out the next set of props. I had a show with over 1500 props once, and this system worked remarkably well.
The added benefit is that I can pack up all of the props into boxes at the end of the night, stack them up and wheel them into a locker.
I also lable everything with the prop name, the show name, the point used in the show etc.
Slightly obsessive compulsive, but it works.
That said, if there are decent ASM's, I let them figure out what works best for them.