Since you ask about issue besides software required that only runs in a specific platform I'll add a few specifics to what Justin said which was an excellent answer. In all functionality evaluations, skill sets available are an important factor in selecting an OS platform. That said, any business environment needing more than simple domain controllers/small network server I believe requires at least one person moderately Linux/BSD literate. My forumlae for selecting servers for functionality are as follows:
Web Servers (Especially PHP based solutions): If have at least 1 moderately versed Linux staff member: (in order of preference) Redhat, Oracle, Scientific Linux, CentOS, Oracle, Debian, FreeBSD, OpenBSD. More server admins know the Redhat based directory structure which are shared by CentOS and Oracle than Debian or OpenBSD. Hence the order of preference. Its faster, more secure, is easier to find answer for any issue via Google search and MS Windows and easier to integrate other technologies scripting for text/file processing. In response to Justin and FreeBSD: Yes its an excellent choice I agree, especially on security although its sometimes not easy to find someone comfortable with BSD environments.
File Servers: If performance and data integrity is a key requirement, Linux (Redhat, Oracle, Scientific Linux, Debian, CentOS). Many large organizations like to use Linux Software RAID 6 for their servers (I do not recommend RAID 5). You may find iSCSI and Apache Hadoop of interest.
Database Servers: If you don't need to integration something into MS SQL Server 2008+ (including Oracle Database), its Linux again. Oracle actually does run significantly faster in Linux. Redhat, Oracle, Scientific Linux, CentOS. I'm not as keen to recommend Debian based distros because I haven't run Oracle in Debian and Redhat based distros are easier to support. If you have mission-critical apps that require top performance suggest configuration on Database partition of RAID 10. Reduces disk bottleneck.
For file sets where ease of access is key, keep a MS Server for easy role based security schemas and integration into the MS windows File explorer, but would keep critical files backed up on an RAID 6 Linux file server. MS windows is not great on software raids and hardware raids can be a disaster when the controller inevitably fails and someone forgot (or too cheap) to buy a spare card ahead of time. Linux software raids are proven rock solid and not hardware dependent.
Security/Firewall Server: OpenBSD or FreeBSD are my first choice. Or a standalone produce based on of these. when it comes to security, better to get someone with the expertise in security and these OS's. Worth the investment.
Virtual Server: Here performance is critical and recommend Linux hands down. Redhat, Scientific Linux, CentOS, Oracle are easiest to support the widest variety of open-source and commercial options. There are some for Debian and BSD distros too, but not as many that can be installed, and some commercial, closed-source solutions that may be ideal cannot be compiled by hand. Know several companies using VMware, XenServer. Proxmox looks very promising as well. VirtualBox is good too.
Groupware/Mail servers: This comes down to software solution choices. If simple MS outlook integration is all that is required and the server administrators are a not intermediate-advanced, its a simple MS Windows server. If you need more advanced options and want to use IBM Domino server for Lotus Notes I recommend a Redhat based distro (Redhat, Oracle Scientific Linux, CentOS) to increase performance. For support purposes Redhat and Oracle are safest to avoid the "we don't support that OS" tag line from people at IBM (depending who you talk to, some are helpful with centOS as well). Novell Groupwise had serious security/stability issues when a team I worked with was testing various Groupware servers; we could kill it with a single e-mail every time and no fix was available at the time of testing but probably fixed by now. The choice here I think comes down to features required, cost allowed, and security. IBM Domino server is expensive but has more features and TONS of encryption options. You can run it on MS windows servers as well, but performance won't be as fast especially with encryption features turned on.
You can see that where storage redundancy/speed/integrity are an factor, I feel a Linux OS is the TOP choice as I've had bad experiences with hardware raid which is the only real commercial level raid solutions available for MS Windows, including their server.
Many people I know swear by performance of Gentoo or Slackware. For situations that require commercial software these I find don't work well. And its harder to find server administrators that know these OS's. Hope all this helps.