The answer is: YES!
Although Nikon does not officially recommend using any kind of AA rechargeables, I wanted to see just how many shots you could get, if a person actually did have to use rechargeables. Many have claimed that AA rechargeables do not work, and the D100 shows a low-battery display (one-segment blinking), then shuts down very soon afterwards. This is a situation where as much information about the batteries need to be explained as possible, so that if you try what I did, you will get the same results. So, let me tell you what I found out...
For the first test, I used GP 2000mAh NiMH batteries. I fully charged the batteries in the NEXcell NC-20FC charger. After fully charging the batteries, I inserted them into the MS-D100, and then into the MB-D100. Initially, the D100's 3-segment battery level indicator only showed 2 segment bars. However, a few minutes passed by, and it then displayed a complete 3-segment battery power level. I was able to shoot 205 RAW photos before the D100 went dead. I do mean dead. There is a bell curve of power for Li-Ion batteries because of the D100's massive power drain (like any other DSLR these days), and using NiMH batteries only made this power curve steeper. When the MB-D100 ran out of juice, it did so instantaneously and without warning. So, for those who are going to use this method, be sure to use the batteries I have used above with the same mAh rating, and the same brand. EN-EL3 batteries are selling for around $50 a piece, and having a few extras on hand is sure worth it. However, I can't help but have a dozen or so AA batteries on-hand and on-demand already because of my flash unit, the SB-80 DX, and most of you will too. Having the MS-D100 AA battery adapter (supplied with the MB-D100) is certainly good for a few extra shots you normally could not get when in an emergency situation.
I am going to do tests on 1800mAh batteries next. I have a few sets of brand new MAHA and NEXcell brand batteries, so this should be interesting. Stay tuned.
I tried the MB-D100 with MAHA 1800mAh and NEXcell 1800mAh, and discovered that you lose at least 35 RAW shots. Today, there really isn't a reason why you should be using 1800mAh batteries because most camera stores carry the 2000mAh and on up to 2200mAh, depending on where you shop. My advice would be to use the 2000mAh batteries so that you get a fairly good amount of shots. Anything less is a waste of time and money.