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Excluding games, most windows programs have a native Linux replacement. You are almost always better off using the native linux app than try to run a non-native app on Linux. On those few programs that do not have a native Linux equivalent (and do not run on wine), you can install VMware (or some other Virtual Machine) and run the app that way.
Guess knowing what program you are asking about might help.
Also there is a way to use all of the files and registry parts that you have in a windows system. You copy them over to a wine install and it might run. People have used it for CS.
Im thinking along the lines of popular workplace applications. Say for example, someone uses Microsoft Office with Outlook connected to an Exchange server. Of course with many businesses you also have proprietary applications too.
Eventually I would like to setup a system similar in operation to Microsoft Terminal Server and have multiple users connect simultaneously.
If you are looking to run Office applications (and possibly support for getting them running) I would recommend Codeweavers - they do a good job providing support and offer excellent software.
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