I think the S2 makes a mighty fine JPEG right off the CF card or Microdrive. The navigation system for making changes to image capture parameters is simpler and faster on the S2 than on the D100. The S2 offers VERY good higher-ISO performance. Especially when shooting RAW files. RAW Fuji S2 files re-sized downward about 50 percent and saved around 9 quality (on the older 10-point scale in Photoshop) make for fabulous 1-meg JPEGs.
One of the S2's strengths I think is its ability to make a much larger JPEG than the D100--around a 4.3 meg file at 4256 pixels on the long axis. These JPEGs can be re-sized downward for some very lovely jpegs or to make awesome prints. This is all done in-camera at the 12 Megapixel size. The D100 does not shoot as large a JPEG as the S2 does. Nobody can dispute that. I personally think the S2's larger inkjet PRINTS are slightly sharper than D100 or D60 prints.
The S2,according to Phil's tests, is currently the king of resolution for cameras actually tested. Phil Askey doesn't empahasize that fact, but instead uses very carefully chosen words and IMHO skirts around this aspect of the S2. Read his review carefully,and you see that the S2 is the CURRENT resolution leader. Using RAW files, the S2 has a slight edge over all competitors,according to my reading of Phil's tests. And indeed, the S2's RAW files DO make some very incredible pictures. If however you shoot in JPEG FINE, as many people do in the real world,for various reasons, the S2 offers a very worthy image,right off the CF card.
As far as flash goes, the S2 does not use Nikon's DX TTL flash system, and for flash exposures at 100,160,200,or 400 ASA/ISO it is generally accepted that the pop-up flash on the S2 works better than the D100's does. Also, most people seem to feel that the S2 does "better overall" on flash exposures,in a wide variety of modes and situations,and with many more flash units, than the D100 does. Frankly, Nikon's DX flash system is not all that perfect in reality, and the number and variety of units that used DX or that have a DX capable module is nowhere near as great as with the older, F-5 sytle TTL Multi-Segment TTL flash metering used in the S2. The S2 offers a higher sync speed and a lower minimum ASA than the D100, but it's no D1-series body, and if you want high-speed action capture,ultra-fast shutter response, a big buffer,and really awesome autofocus, you'd better consider a D1-series (D1h or D1x) body. Keep this in mind--niether the D100 or S2 are really,truly,totally professional cameras for high-speed,ultra-demanding use. But they are affordable,light,small,and do deliver good images. If you need hi-speed flash synch, look long and hard at a D1-series body.
No camera is perfect....The S2's battery needs put a lot of people off. The lack of a vertical release is also a sore spot. If you need to use a battery-hungry lens like the 80-400VR as I do, the need for 123A lithiums becomes a pain in the butt. The S2 also has no factory-made AA-cell external pack, but the D100 does. Battery life on the S2 is excellent,it really is. And the D100 has a most capable "pack" in a one-battery system that's pretty sweet.
I don't have a non-disclosure agreement with Nikon, the way some forum members do. I do not work for Nikon in some roundabout way or write professionally about Nikon equipment, nor do I host a website devoted mainly to Nikon equipment. I don't receive items from Nikon for testing and for writing reports about.I'm not crossing forums either, trying to dissuade you from buying a Fuji,nor am I trying to refute positive comments about Fuji, the way some forum members are doing. I own Nikon and have shot it for over 20 years. To me, the S2 is a Fuji-modified Nikon, and frankly I felt the S2 was a very slightly superior camera than the D100. So I bought one,with my own money. You could do good work with either camera. I just think the S2 has a slight edge in several areas like flash and in-camera JPEG, as well as absolute resolution. I do prefer working with Nikon's NEF files, and Nikon Capture is a better way of processing RAW files than EX Converter, but there's always some bad with the good.
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Happy Shooting!
Derrel