Linux-friendly messaging and collaboration servers do exist, but switching may not be a realistic option. The business risk associated with replacing a heavily loaded Exchange Server may simply be too great. Also, inadequate integration with Active Directory, for example, can hamper Linux in a corporate environment.
Frustrations like these are inevitable: This is vendor lock-in at work. As a general rule, the leading Linux applications support most of the functionality that users expect from their categories, but proprietary protocols and closed APIs can thwart true compatibility. To expect a one-to-one replacement for every feature of a specific commercial application would be unrealistic.
The same holds true even for basic desktop productivity software. For example, Linux applications handle files saved by Office 2003 and earlier well, but they still lack support for the newer Office 2007 file formats. You'll need to examine the actual workflows within your organization carefully to determine whether it will be feasible to migrate away from Office. Ask tough questions.
Bridging Windows and Linux
You may find that certain employees rely heavily on specific Windows software for which there is no adequate Linux equivalent. In such cases, you have several choices, though none is ideal.
One option is to configure desktops as dual-boot systems, which allows the user to select either Linux or Windows from a menu at startup. This isn't very efficient, however, and it can also be problematic; for example, files created under Windows will be accessible from Linux, but not the other way around. Don't be surprised if users lapse into old habits and spend most of their time in Windows.
Another method is to install virtualization software for Linux, such as VMware Workstation or Xen, and run Windows inside a virtual machine. This will allow users to access the Windows applications they need while still performing most of their tasks using Linux software.
These alternatives present two big problems, however. First, they both require a licensed copy of Windows for each machine, negating any cost savings of Linux. Second, they effectively split each workstation into two complete systems, doubling the IT management workload. Because of this, neither method is a viable long-term solution, so should only be used as a stopgap measure while you phase out Windows.
A third solution is to use Wine, a Windows compatibility layer for Linux that allows many Windows applications to run as if they were native Linux software. Not every application works properly with Wine, however -- you should consult the project's application database to see if your software is compatible. A commercial version called CrossOver Linux, which offers additional installation and runtime support for selected applications, is also available.
Finally, a number of thin-client solutions, available from such vendors as Citrix and Sun Microsystems, allows Windows applications to run in terminal windows on Linux desktops. This method has the additional advantage of favoring lower-end hardware. Be aware, however, that most such solutions will require additional infrastructure investments to get up and running.