I had this recording time problem too the first time I used the D100. The camera is probably compressing the .NEF images and that takes considerably longer than just recording the RAW data (my experience was a 40 second lag after each exposure, when the buffer was full). When shooting uncompressed and the buffer is full the .NEF format has the lag or record time around 6 seconds on a 1 gig IBM Microdrive. Unless you have low capacity recording media you shouldn't use compression. Go to the Shooting Menu>Image Quality>RAW>NEF(RAW) NOT RAW Comp.
Now to the .NEF format Issue. I used to live in the darkroom and really appreacted a negative correctly exposed and developed. But I have almost never seen a piece of film that couldn't use just a little more tweeking (I'm away the perfectionist). Today the final output is not always a physical print. The image may go to the web in the form of a .jpg or to print on a press in the form of a CMYK .tif. The advantage of the .NEF format is, that all the information is in the file, nothing is filtered out or left behind. This allows for the greatest latitude of interpretation in creating a print, or web image, or what ever the use maybe, just like a properly exposed negative. Darrell Young is correct when he posted above "Any format that moves away from RAW (NEF) format is throwing away data." In fact if you SHOOT in anything less than .NEF format you are throwing away data. Data that you may want, or need later to improve, change or correct you image.
But I believe that Mr. Young is on the wrong track when he states, "The TIFF format is an 8-bit format that comes from that same RAW 12-bit data. It is 1.5 times larger than NEF, but contains less image data. In the case of TIFF, the conversion from 12-bit to 8-bit crams 12-bits of data into 8-bits of data space. That is no big deal, since there are no devices that I know of to display the full 12-bits of data anyway. Even the monitors we use can only display 8-bits, so you never really see the full 12-bits." It IS a big deal if you want to keep as much data as possible, as you should. Keep in mind that even though we can't see a 12-bit per pixel image on our monitor, because we are limited in the total number of colors and shades of those colors we can discern and the monitor can display (8 bits per pixel or 24 million plus colors). But the DATA is there. If we change a 12-bit per pixel image, lighten, darken, alter the curves or any number of other corrections it can effect these unseen extra bits of data that can and may be use by software to create a truer, more accurate and consistent representation of the image and or more consistent final output. After all why do you think they manufacture "True 48-bit color depth" color scanners (keep in mind that's 16-bits per pixel instead of 12-bits). I do agree with Mr. Young when he states, "So, if I were going to use a format for printing to photo paper, it would be TIFF. It is a loss-less format in that, once the 12-bit per pixel to 8-bit per pixel conversion is done, there is no more data loss. You can modify and save the image many times with no data loss, since no data compression is taking place. (like with the JPEG) format. The TIFF format is a widely used loss-less format. The only real drawback is that it is HUGH. A 9.5MB RAW file will convert to a 17.6MB TIFF file." Keep in mind that you can use a standard loss-less compression routine to slightly reduce the file size, and HUGH, after all is a relative term. And again I completely agree with Mr. Young when he states later in that same post, "I use RAW (NEF) format extensively, since I want ALL of my original data to be there when I decide to work with an image. JPEG throws away an enormous amount of data. TIFF throws away some too. So, wouldn't it be better to shoot and store your images in NEF. Then when you want to do something with the image in the future, you can simply make a TIFF or JPEG out of it. You will, like a negative, always have your original pure data to work with. " Well stated.
So, match your FINAL file type to you FINAL output, WEB - .jpg, PRINT - .tif, and so on, but shoot to get as much data and resolution as possible. You can always throw it away, but you can't create it, if it wasn't there to start.