If you're looking for the right solution to your problem, advancemame would be it. If your looking for a quick and easy solution, set your pc monitor refresh rate to 60Hz. This will fix your problem for almost all games. If you're having trouble with a game that uses a wierdo refresh rate like mk, then you'll need to either add a custom mode to your video card settings or use advancemame.
As far as stretching goes in the official mame, there's a configuration parameter (which I don't recall off the top of my head) that forces integer stretching. Integer stretching is as close as you can get on a PC monitor to authentic emulation, however, unless you are using advancemame (or a custom set of modelines) the game may not take up the whole screen.
If you're looking for a little more detail read the modeline tutorial on my site. Right now there isn't any info on creating custom modelines for Windows, however, google should turn up something should you be interested in going that route.