Depends on what you want to achieve... The three major schools of thought are something like 'pixel perfect', 'enhancement', and 'lolwut? I don't care'.
Some people prefer to have the systems displayed at the exact pixel ratio of the original systems with no visual modification. This involves either running your monitor at the original resolution (Which cannot be done for most resolutions on a 31kHz monitor), or at some exact multiple of the resolution (eg, exact doubling such as going from 320x240 to 640x480). An exact integer scaling is essentially visually identical to the original resolution. If you only have a handful of standard resolutions installed on your computer (640x480, 800x600, 1024x768, etc) then the various resolutions are going to not fit exactly and thus have boards around the image.
Enhancement is using any one of a number of algorithms to attempt to compensate for the differences in resolution by creating additional pixels to smooth out edges. With this technique, usually the more resolution you give it to work with, the more pronounced the effect will be.
Then there's just not caring.. This usually means bilinear filtering, or non-filtered but stretched with weird artifacts. But hey, you can still play the game, amirite?