<p>How do you run Emacs in Windows?</p>

<p>What is the best flavor of Emacs to use in Windows, and where can I download it? And where is the .emacs file located?</p>

Well, I personally really like what I have been using since I started with Emacs, which is GNU Emacs.  It looks like it is built for
windows too
.  That link also answers your
.emacs file question
.
Here is a place you can download it
.  You should probably get version 22.2 (the latest).
If this is your first time, I hope you enjoy it!  I know I absolutely love emacs!