First, I'd like to start with an apology for writing a novel.. I do recommend checking out the reviews on DPReview.com in addition to what I have written below.
In my opinion, it all comes down to finding what meets your needs. I've seen fantastic work out of the D100 and the S2 up to 24x30 prints. I couldn't see the difference between them at that size.
I was a Fuji S2 owner but switched to the D100 and haven't looked back since. The main reason I switched was an issue that my S2 had where it would focus on the background instead of the subject. A few very seasoned pro's had the same problem. We all switched the D100.
Besides the fact that I have no focus issues with the D100, what I like about it over the S2 is:
- The rechargeable battery that comes with the camera is good for about around 1000 shots with the post-view enabled.
- The grip is better in my opinion and adding the MB-D100 is much better than adding an MB-16 to the Fuji S2. I use the portrait grip buttons on the MB-D100.
- With the MB-D100 you can use 2 of the EN-EL3 rechargeables for even more shooting time.
- I haven't seen the need to clean the sensor yet after 5000+ shots. The Fuji seemed like a dust magnet.
- RAW (NEF) files save a LOT faster on the D100. Using a Lexar 40x Pro card an uncompressed RAW file saves in about 6 seconds. The Fuji was way to slow if you were shooting anything that was alive. Playback of RAW files is much faster on the D100 as well.
- The D100 uses USB to connect to a computer. It works okay but the S2 uses FireWire which is very nice.