Wine is a compatibility layer that allows you to run many windows programs in Linux. It would be installed after Ubuntu using Ubuntu's package manager.
If I were you I would test this all out on one machine before you make any final decisions. There are MANY microsoft programs that just will not run using Wine (Microsoft Visual Studio is one) and many times, even if a program runs it may not run as well as it would in Windows.
Like I said, if you depend on windows software and need that software to run as best as it can you really should just run it in windows. I cannot be more specific as some of your programs you allude to sound like they were programmed by your own folks.
Also, are these server apps or are you talking about workstations? The more details you give about the apps/types of apps, the better answers we could get.
Also, to get an idea of how some programs work/don't work using Wine check the AppDB
. It has a great deal of info. Although somewhat old, here is a snippet of info from the appdb on Visual Fox Pro