First off I just want to thank you all again for all your responses, this means a lot.
Okay so somewhat as expected my options are basically VM or Wine.
As I mentioned I haven't tried these options out yet so I can't really say that they are not effective for me. (After reading most reviews on other "Wine" based products it seems most say to stick with Wine itself).
I am okay with going these routes, like I said I am just looking for a little more of a way to make the VM a little more hidden. When you think of it, the hard part seems to have already been done, which is getting the VM to run Windows within Linux, the next part is a graphical way to make it appear to be just part of Linux (not to say this is easy).
Now TobiSGD's response (thank you) is pretty interesting and it is a little closer to what I am looking for (I was not aware of this option). When you follow the link given it shows an environment where Linux windows and Windows windows are playing together, sharing the desktop.
The only weird part about it is that you have the Windows XP taskbar on top of the Linux taskbar, and in the Linux taskbar you have quite a few extra items there "virtualbox seemless", "virtualbox ose", "winxp running". Not a huge deal but it would be pretty cool if these things were hidden a little more.
I am sure Linux has it too, but a good example (little different scenario) is like in Windows when you go to open up a file you can set and or select what program you want to open that file with.
It would be cool if you could in Linux set a Windows program to open with a VM program so that it just opens up a window of that Windows program within Linux. In essence hiding the middle man that is the VM program.
I am aware that I may be restating things but with all of your responses it gives me more to work with in explaining things in different ways.
Again thank you all, all responses are appreciated and welcome.