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Nick Geht, the owner of FlexHood Products has put together a short list of tips for using flash with the Fuji S1. With his permission, here's my annotated version:

1. Use only ISO 320 & 400.
   
   That's because the N60 body that the S1 is based upon can only calculate TTL exposures for ISO values up to 400. In general, all Nikon bodies have a top end for TTL calculations, and you need to be aware of what that is, as most bodies won't stop you from setting something outside the range. That's especially true with the S1, which has separate digital and camera controls.
   
   
2. If you are not using 'custom' white balance the camera uses a special white balancing mode if the flash is ON, regardless of the white balance mode you've selected.
   
   This can be good or bad news, depending upon the mix of light under which you're shooting. It also means that the trick of putting a theatre lighting filter over the flash head to balance the flash against existing light doesn't work as well on the S1 as it does, say, on the D1.
   
   
3. Lithium batteries are required for the built-in flash to work. Built-in flash does not work with the plastic dummy inside.
   
   The internal flash is part of the camera body component that Fuji didn't modify, and the internal flash gets recharged by the lithium batteries.
   
   
4. TTL exposure compensation is possible with the S1, as the exposure compensation controls both flash and ambient exposure. If you put your camera in manual exposure mode you can manually control ambient exposure and use flash exposure compensation at same time.
   
   This tip needs a bit of explanation. When the S1 is in the flash mode that Nikon refers to as Matrix Balanced Fill-Flash (MBBF), the camera adjusts the amount of flash output based upon its calculations for the ambient exposure. If you dial in a different ambient exposure using exposure compensation, the flash output is also varied. Unfortunately, you have no way of knowing what that variance is.
   
   Be aware that manually setting exposure compensation and flash exposure compensation simultaneously in MBFF mode can be a frustrating and self-defeating practice. As you dial in more and more compensation, the camera will at some point get confused. I've watched users dealing with underexposure try to dial in several stops of + flash exposure compensation, only to have the result be something that's even more underexposed! If you use the MBFF mode, try to use only camera-based exposure compensation, if possible.
   
   If you want to more closely control the ambient/flash balance, put the flash into Standard TTL and use manual exposure mode instead. Then, if you want the background slightly underexposed, make your ambient exposure slightly underexposed (the flash should still fire correctly). If you want the flash to be used as fill (not as the primary light), then dial in -1 to -2 stops of flash exposure compensation and leave the ambient exposure unmodified from the camera's recommendation.
   
   
5. Fill flash outdoors is a challenge. With a maximum flash sync speed of 1/125 and a minimum ISO of 320, the "Sunny 16" rule means you're at roughly f/22 for the ambient exposure. Manually zooming an SB-28 to 85mm helps to squeeze the maximum power for outdoor fill flash.
   
   You want to preserve all the power of your flash, as it will take a fairly bright flash to provide fill in outdoor light. At a minimum, make sure that you zoom the flash to as close to 1.5x the actual focal length used as you can get (e.g., a 50mm lens on the camera means you should have the flash zoomed to 70mm). If you don't need flash across the entire scene, then zoom the flash further (and make sure that it is pointed at the area where you want the fill to appear). S1 users should also carry neutral density filters with them. By putting a two-stop ND on your lens, you get close to the settings that you'd be using at ISO 100 and a camera that syncs to 1/250 (i.e., what most of the rest of the world enjoys...).
   
   
6. Because of limitations in the N60, the camera does not supply the ISO, aperture and focal length information to the flash. Thus, it is pain to keep them in sync manually when you use an external flash in automatic mode.
   
   Indeed, automatic flash mode is something I avoid with the S1, for that very reason. Note that with most newer Speedlights, the only time you get a chance to set the ISO value is when you turn them ON, which makes using Automatic flash mode even more frustrating.

Fuji Digitals Do TTL

Unlike the Nikon digital SLRs, the Fuji S1 (and upcoming S2) allow TTL flash with virtually any Nikon-compatible flash (i.e., you don't need a DX flash model, as you do with the Nikon D1 series or D100). That means that pre-flash is cancelled if you tilt the head or remove the flash from the camera.

Just remember that the TTL sensors in the camera body haven't changed. They still see outside the CCD area (they see the original 35mm frame area). That means that large bright or dark areas just outside the frame can have an impact on the flash exposure.

So why do the Fuji bodies get by without a DX flash when Nikon digital SLRs don't? Good question, but it probably has to do with the reflectivity of the filter over the CCD. Fuji either made an attempt to imitate film reflectivity, or they just got lucky.