I have been a fan of linux for about a year and I am very happy with it. I just have one question to ask and I hope someone can help me with it.

To the best of my knowledge windows "knows" what software is installed on the system. Does Linux have this as well besides 'rpm -qa'. Maybe this is a hard question to put into words but windows is intuitive about what software it has installed on the system despite what installer you used to install the software (Wise, Installshield). Does that information get stored into the registry in windows.
I try to install all of my software under Linux from source code because not everything is in RPM format and mixing source and RPM can cause problems. But how does the overall system know what software is installed on linux without a central "registry".
It's like installing software in windows with and without an installer. If I install The Sims the system knows it's there it has links, an uninstaller and registry entries. but if I download a zip file and unzip the file sometimes it doesnt have a setup.exe or install.exe but just has the files it needs and the executable program.exe. now granted I can run program.exe but the system cant see it.

So my main question is does linux have a way to keep track of what programs are installed?

Most windows installers write to the registry, which is how windows "knows" what's installed. If you want the same functionality in RedHat, build all your software into RPMs before you install it. The package manager is how the system keeps track of software.