The filesystem has nothing to do with it, it's the binary format they use for executable programs. It's been a long time since I've had to pull this info from memory, but I think Windows uses PXE format, and Mac OS X uses ELF. The filesystem is just the means by which the operating system catalogs and stores files. So Windows may use a series of three drawer filing cabinets with plain manila folders, while Mac OS X may use five drawer cabinets with multi-colored folders. But at the end of the day, a TPS report is a TPS report no matter where it's stored.
Data will transfer just fine, it's really more a matter of whether or not you can find a program that will be able to read that particular file format. I find a great many people who end up saving things in the new OOXML format of Office 2007/2010, and so about the only way you're going to get those files to open is with Office 2008 on a Mac, since Microsoft deviates from their own specification whenever they feel like it. IIRC, Office 2007 was tested and found to be the worst in terms of compliance with the OOXML spec of all apps that claimed to support it.
But plenty of apps will have direct Mac counterparts. All Mozilla software, like Firefox and Thunderbird, iTunes started as a Mac program, VLC Player, OpenOffice, MS Office (and, I might add, puts the Windows version to complete and utter shame)... Then there are plenty of really good alternatives to programs. Adium is one of the best IM programs I have ever used, it's just a shame development has really slowed on it lately.
It's not quite as dire a situation as you're painting. There will be some teething pains, but nothing quite so dramatic as you seem to be implying.