Several options:

- Wine emulates the Windows API and hence allows you to run (some) Windows programs on Linux. The Windows programs don't know they're running on linux.

- VMWare, Plex86 and Bochs actually emulate x86 hardware, and hence you can run a "Real" copy of Windows on the emulated hardware. Much more accurate, but slower and requires a real windows licence.

Wine will not allow programs running on it to store their files on an NTFS partition (until there's a real writeable NTFS driver for Linux anyway) - however they *can* store their data on any other type of partition Linux supports (ext3, etc) without noticing the difference (actually they might "see" it as a FAT or FAT32 partition)

The hardware emulators will provide a "virtual disk" on which you can run whatever filesystem the version of Windows you use supports. To use native storage you may have to "Network" mount it via samba.