The included NikonScan software for Windows & Apple Macs is a good starting point. It will probably be sufficient for most user's needs and is recommended for new users. With the settings at "factory default", NikonScan will generally produce excellent scans and provide a useful reference point for further experimentation. Various editions of NikonScan can work with all Windows versions and early MacOS versions & hardware; see below for details.
Both alternatives to NikonScan are "paid-for" packages which may offer more functionality but at the cost of complexity. VueScan supports a vast number of current and legacy document and photo scanners. They offer an unlimited free trial download (with watermarked scans) and a good value purchase price. Silverfast offers model-specific software aimed more towards the professional user with options such as IT8 calibration using their target media.
Article ID 000002288:
(Computer System Requirements for Nikon Scan software)
Version 4.0.3 was the final release of Nikon's Coolscan scanning application for Windows. It was intended for the 32-bit Windows Vista but also runs without modification in the 32-bit versions of Windows7 and Windows 8. Nikon did not produce Coolscan drivers to run under any 64-bit version of Windows but with some fairly simple manipulation of drivers, version 4.0.3 will run under all modern Windows versions. Note that on Windows XP, version 4.0.2 is needed which is functionally identical.
My notes detailing the 64-bit work-around procedure may be found here: NikonScan in 64-bit Windows - Detailed Instructions. The original driver work was done by "steel chn", a member of the Photo-net Digital Darkroom forum; if interested you can see the very lengthy thread here.
NikonScan version 4.0.2 was the final release of the MacOS software and the last supported MacOS version was 10.4.11 running on PowerPC Mac (Intel variants are not supported). There are some reports of users running later versions and different hardware but possibly not reliably.
Unlike the Windows situation, there is no known work-around to allow modern Macs to operate with the Mac versions of NikonScan. However it is possible to run a Windows OS on a Mac and then Windows NikonScan within this. One technique is to run a "virtual machine" and another uses Bootcamp. The following notes describing these techniques were kindly provided for publication here by Coolscan user Russ Meacham in Australia: Two techniques for running NikonScan on a modern Mac - Russ Meacham
As a repairer, I am regularly discussing user's problems that may be either hardware or software-related. When the user is running NikonScan, not only are the error messages more explicit than other software but the single "Factory Defaults" button quickly establishes a known state. Additionally, where the user is running third-party software and problems arise, the ability to cross-check between this and a NikonScan installation is invaluable. I'd therefore recommend that all users, Windows and MacOS, have a NikonScan installation regardless of what they use routinely.
Consider obtaining an old (and cheap) laptop on which you can install a contemporary operating system and the appropriate NikonScan software. As a stand-alone scanning system without a network connection there are no security issues with running a legacy OS. For Windows, look at a 32-bit PC with XP or 32-bit Windows7; for Mac look at a PowerPC with MacOS up to 10.4.11 (it must be a PowerPC and not an Intel processor machine).
Further Information:
I am based in Lincoln UK If you have a Coolscan scanner in need of service or repair then please contact me by emailing coolscanuk@gmail.com (Please be aware that due to the volume of work, emails may not be answered immediately and I have a lengthy waiting list for scanner repairs.)