That task is easier than it used to be, thanks to Web development technologies and ODBC/JDBC (Java Database Connectivity), but it's still a challenge.
How To Make It So
The first step in attaining cross-platform competency is to divide your programmers into two groups, according to expertise. One group should comprise UI (user interface) programmers who specialize in developing Web pages and presenting your data on your preferred platform, using your Web development tool of choice.
The other group should consist of programmers who develop back-end applications and write system interfaces. These folks must be proficient in the development tools used for both Windows and Linux (or at least some form of Unix)--or they'll have to become proficient fast--because they'll need to write code that can run on whichever platform is most cost-effective for the organization.
Of course, given that annual Linux licensing fees total a big fat $0, the need for training isn't likely to stop many organizations from moving a growing number of applications to Linux--the transition will just take a little longer if you have to start from scratch.