We will be there on very similar days to yours (9/3-9/7)! Though it's been years since I've been to DLR over Labor Day (it was back when DLR was just DL), I think I can answer many of your questions based on conventional wisdom or give you some excellent threads where you can read up to your heart's content.
Which rides would you hit during MM? Is MM only at DL and not DCA?
Yes, MM is only at DL and not DCA and it's typically held on the "S" and "T" days (Sunday, Tuesday, Thursday, and Saturday). With the 5K being held on Saturday and the half-marathon on Sunday, this may change, so keep your eyes open. Many people choose to take advantage of MM to ride Peter Pan which can build lines of 30-45 minute minimum waits just shortly after the parks open. DLR29 has an outstanding Superthread all about Magic Morning and gives not only his suggestions on which attractions to hit first, but also many other tips and techniques to get the most out of that valuable time. See
DLR29's Magic Morning Super Thread.
How have the crowds typically Been in the past? I know this is the weekend of the marathon- will it be mobbed?
With the advent of the million+ annual pass holders, conventional wisdom about crowds has been flipped on it's head. When you look at the AP blockout dates, September 4th and 5th (Saturday and Sunday) are blocked for all but the premium APs. This means Thursday, Friday, and Monday of your stay are likely to be the most crowded. This is particularly true for late afternoon and evening hours. So make the most of the early park hours on those days especially! Although there will be many people there for the Half-Marathon weekend, the numbers of runners is actually smaller than many conventions (5000 half-marathoners and I'm not sure how many for the 5K and Kids' Fun Run). Speaking for myself, I may be wanting to lounge by the pool all day after running 13 miles Sunday morning especially since I'd have to buy a blockout pass to get in on my Deluxe AP.
Here's some advice from one of the other Disney fan site's about last year's Labor Day weekend and news, tips, and hints on how to make the best use of your time for the weekend --
Runners Take Over Disneyland.
How late do the parks usually stay open? Do we think there will be 2 showings of WOC? And which day would be better to see it? In thinking sat would be busier but I don't want to chance waiting til sun and having the chance that rain cancels the show and we don't get to see it at all..... I will be booking WOC dining package at AG. Opinions from past labor day weekenders please!!
Here's the link to Mouse Planet's DLR Update from Labor Day last year. If you scroll to the bottom, you will find the park hours from last year and this year's hours are likely to be similar (though with WOC DCA's hours may expanded).
Labor Day 2009 Park Update
As to when to see something you really want to see, I'm a HUGE proponent of HydroGuy's Fireworks Rule. Do what's important to you early in your trip!!! You never know when weather (rain's not likely, but wind and fire can still have an impact at times), mechanical malfunction, or any other number of things can interfere with your plans. See
HydroGuy's Fireworks Rules. If you haven't already read through all of HydroGuy's threads, I can't recommend them highly enough. As many other people in the past have commented, they outshine the best DLR guidebook by lightyears. It sounds like you're a WDW vet, so you should definitely read
HydroGuy's DLR Guide for WDW Vets.
Have fun and keep an eye out for any LGMHs!