No I don't use commander mode. Not to say that you can't, but it probably has to do more with my equipment. In the past, I shot a lot of action sports including skateboarding, BMX, MX, etc. as well as studio stuff. The choice for portable flashes were (and still are to some extent) Sunpak 555, Quantum Q Flash, and Nikon SB-28 among others. Because of the combo of flashes, not all were compatable with this new Commander system which hasn't really been out that long. Also, it was important to shoot sequences with strobes that could keep up. With Sunpak 555, you can turn the power all the way down to 1/64th of full and shooting around 800 to 3200 ASA you can shoot full sequences at 8 frames per second and the flashes can keep up. Of course this was done with film cameras, in my case the F5. We'd often shoot Kodak 1600 B&W and push or pull too. Now in order to do this, we had to shoot with 2 or 3 slaved flashes in order for there to be enough light, but still cycle enough. Problem is only a few radio slaves could keep up. Quantum Radio slaves are pretty good, but only come in 4 channels, which isn't good when shooting with other photographers at a big event, etc. That also means no optical slaves that can be triggered by other flashes on other cameras including point and shoot cameras. Pocket Wizards are good to, but won't send a signal at 9 frames per second. The Pocket Wizard Max will do all this and have little radio interference. The older Radio slaves were plagued with radio interference coming from Supermarket automatic door openers, etc. Also, on shoots including shooting at places like LA where the Lakers play, there are built in overhead strobes that photographers have to use so that they don't blind the players and a nice studio lighting for all the pro photogs. If you look at Sports Illustrated, you'll notice the lighting is very consistent and perfect every time. They just clear you for the frequency and you are set, no flashes necessary, just MAX. I also use the system in the studio with my studio strobes. Lastly I also shoot with a Hasselblad, so I use the same strobe set up. Basically to answer your question, you could use the commander mode, but I have little to no experience with it and haven't pursued it more due to it's limitations for what I need. Your needs may be different. BTW a D50 can use Commander mode if you buy the appropriate hardware.
http://www.kenrockwell.com/nikon/su800.htm