A late reply, but as the saying goes.... I have a Nikon coolscan 9000 and have had no problems to date. Only got the 9000 because I need to scan medium format as well as 35mm. Plus, I'm a Nikon diehard... Bob PS- Should you require any additional info. don't hesitate to ask.
I also have a Nikon Cool Scan Scanner, of the 9000 version, however only have Mac equipment and have had a hard time getting it to interface with the scanner using the original s/w running with PC Parallels. I've tried other s/w packages but have not been happy with results. Any thoughts? Bob
Mac only here, no parallels. Nikon Scan 4 stopped working a few operating systems ago. I've been using VueScan Pro (~$90) for the Coolscan 5000 (iMac 2009, 10.8) and am quite satisfied with the program's ability to get the scanner to work close to or at optimum. Even if there is nothing else to be said for it, it comes much closer to being a user-friendly program than SilverFast (which I tried and, sadly, detested - slick website, though).
A flatbed document/film scanner will never achieve the output quality of a dedicated film scanner, especially with scanners the quality of Nikon. I say never because scanners are not getting much attention from design teams these days. That is not to say the Epsons are excellent scanners. They come really close to the film scanners and are more versatile.
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Since the Nikon Coolscan 5000 is a 35mm film scanner I'm assuming that is what you wish to scan. I believe you will be much happier with 35mm scans from the 5000 (or other 35mm film scanner) than those from a flat bed scanner. Flat beds can do a good job with medium format film and larger, but generally lack the resolution needed for smaller formats.
When scanning 35mm film, I always choose the Nikon Coolscan (V or 5000) over the Epson V750. The results of the Coolscan have the edge over the results from the Epson V750. Not that the V750 result are bad, but the dynamic range and the sharpness is a better with the Coolscan.
I definitely prefer the Nikon Scan Software over the Epson Scan software, which I find quite annoying.
I'm running Windows 7. As Nikon Scan will not run under Win 7 I searched the net and found a proposal how to make a change to the Nikon driver. It actually meant that Nikon Scan suddenly became a very stable program, compared to how many problems I had when running with Windows XP.
Another vote for the Coolscan 9000. And for the same reason. I have a big pile of medium format negs and transparencies, plus my grandfather's 3500-ish slides (mostly Kodachrome), from mid 1930s until early 1970s.
Silverfast makes incredible software for the 9000. (It's also expensive to get into the club, even for their more basic packages... but upgrades are relatively cheap.) That's what I use. Nikon's Mac Software for the 9000 was mediocre at best, and they quit supporting MacOS early on. Silverfast offers much better control, letting you make adjustments during preview, which the Nikon software didn't do. (You had to make a full scan to discover what you'd mis-set! <g>)
I also have 4x5 and 8x10 negs and transparencies to scan, and I use the Epson Perfection v700 for those. It does a good job. (I've never used it to scan 35mm or medium format.)