Some version of Windows XP is probably the best choice. Be sure Service Pack 2 is installed; Service Pack 3 is scheduled to be available sometime in 2008. Even with Service Packs, you still should have weekly updates applied to Windows.
Microsoft says it will stop supporting XP SP2 in April 2009, and stop selling XP of any type in January 2008. By then, new computer power should roughly have doubled.
XP Pro is most flexible. XP Home is cheaper, but does not have some remote technical support options that may be quite valuable to a fishing vessel with computer problems.
Avoid Microsoft Vista unless you have a special application that needs it
Out-of-the-box Vista is generally more secure than XP, but proper tuning can make XP as secure as commercial Vista.Vista can take at least twice the computer resources (memory, processing) as XP, and may need additional video processor (high-end laptop or card in tower/desktop)
LINUX can be extremely effective but probably won't run common fishing industry software applications
The KNOPPIX subset of LINUX sometimes can be used to bring up a Windows computer that won't boot. Considerable knowledge is needed to use it. It fits on a USB stick.
If you have vessel-specific requirements, such as remote control of electrical devices using X-10 interfaces, or scientific data acquisition, a LINUX computer may complement one used for more general fishing functions. Typically, you need half or less of the computer resources that an equivalent Windows installation, so this can be a way to recycle older computers.