The main file shares on our network are currently hosted by old Apple XServes. I had planned to replace some of these with Windows shares as I have better hardware available but have been told this is likely to cause issues with some of our Mac users.
What sort of issues am I likely to run into and what are the recommended ways of hosting general file storage in a mixed OS (Windows, OSX, occasionally linux) environment?
To connect to Windows share most Linux distros uses the Samba implementation of the SMB protocol.
Apple uses their own SMB implementation derived from FreeBSD smbfs in OS X. Mac OS X 10.5 supports SMB singing, having to turn off digitally sign all communications in Windows server 2003 will only be needed for 10.4 and below.
I use both everyday to connect to windows shares and never have a bit of trouble.
On the Macs in question it's worthwhile to note that you should try and disable the creation of .DS_Store files on network shares if you have not done this already. (Details at MacOSXHints.com)
Additionally you should be aware that over SMB you will notice ._FILENAME files created - this is how OS X maintains the resource fork data and such on other file systems. This can cause an issue for someone on a Windows based machine if they try to open up the wrong file.
It's possible to have the server not allow these files (in smb.conf you can set veto_files=._*) but where it is in Windows Server 2003 I'm unsure but I believe using this article from TechRepublic should prove a worthwhile starting point.
Windows 2003 and up have a feature (which is enabled on Group Policy under Security Options) that will digitally sign all communications on the Microsoft network server. That will prevent Mac OS X clients from accessing shares on a Windows 2003(+).
If you can live with the security 'downgrade' that turning that off would represent, I do not see any other issues at all.
Are any of the Mac users using the current XServe -shares for Time Machine backups? IF so, you will need a replacement that supports the AFP -protocol, SMB alone is not enough. Microsoft dropped the last bits of support for Macs on 2008 server, although on 2003 it was already buggy and incomplete.
If the Time Machine -backups (or any other AFP -dependant service) are a requirement, you can either get a Mac Mini server or buy a separate Mac -enabler service for W2008.