One of the more difficult things to understand in conversion of DVDs to mp4 or mkv is the use of anamorphic encoding that is found in DVD-video.
DVD-video stores the video in standard resolutions, and there are only certain sizes that are accepted. The resolutions normally seen in commercially made DVD's are 720 x 480 (NTSC) or 720 x 576 (PAL). You'll see that the ratios for these resolutions are 1.5:1 and 1.25:1. But movies are not filmed in these ratios. Widescreen movies are made in many different ratios, including 1.78:1 (16 x 9), 2.35:1, 1.85:1, etc. See this explanation at Wikipedia.
The actual display from a widescreen anamorphic DVD is therefore not 720 x 480 or 720 x 576...your player will output in a wider view...the display resolution.
So when converting to mkv or mp4, you have to make a decision on how to deal with this. It is possible to use anamorphic settings in a program like Vidcoder, but there is no guarantee that your equipment will be able to recognize this format. So many use square pixel output instead.
While reading at Videohelp, I came across an explanation that I like, from a member there named hello_hello. http://forum.videohelp.com/threads/361709-RIP-and-Convert-to-720x756?p=2295816&viewfull=1#post2295816