I have looked on the net and have found nothing about any programs, or
even a mention that it is possible to convert windows programs into
Pocket PC programs, preferrably Pocket PC 2003.
I need to know if this is possible (it seems like the main issue I see
is changing the mouse input on windows programs into the tft input on
PPC.)
I would like to know if there are any programs out there that CAN do
this. If so, what are they. Also....are there any other ways to
accomplish this goal?

Hi imawonderin-ga!
As far as I'm concerned, there is no way to do this as of now. Of
course there is a fair share of programs that were ported from Windows
to PocketPc, but there is no program that will magically convert the
source code which was intended for one operating system to the other
without some sort of emulation. In a page at Microsoft's website
(Bottom of Answer), you can see that it is possible to emulate the
PocketPC's less complicated architecture on your normal desktop
computer. Hopefully this will spark your interests and you will begin
to code programs of your own. I remain convinced that it will be a
LONG time before any program like you are requesting surfaces.
Although not what you asked for, you may want to consider changing the
operating system present on your PocketPC. I know Windows 95 has been
put on a pocketPC before. Doing so would increase compatibility with
several programs. Here's a link to a forum thread you might want to
consider checking out (Sorry it couldn't be more official):

Forum Thread About Windows 95 On A Pocket PC:
http://www.pocketgamer.org/showthread.php?s=&threadid=3660

Pocket PC SDK:
Phttp://www.microsoft.com/downloads/details.aspx?FamilyID=5c53e3b5-f2a2-47d7-a41d-825fd68ebb6c&displaylang=en