Well, assuming you're using Handbrake...
Usually, if the episodes have their own titles, they will appear chronologically on the title list. Sometimes they won't be easy to pick out (it's not uncommon for commercials or bonus features to be higher in the title list than the episode), but once you find one episode, the episodes below it should be sequential (i.e., if episode 1 is Title 8, and there's another episode on Title 9, that one should be episode 2).
To be sure what title contains which episode, I'd open DVD player and play the individual episodes and see what title the DVD Player application displays. You can do this by clicking on the small window inside the virtual remote, while the "Title" option is highlighted, until the display shows a set of numbers in the format of #(current title)/#(total titles).
Some TV on DVD DVD's include a larger title that contains all the episodes either in addition to or in leu of the individual titles, but the episodes are separated with chapter markers. If this is the case, you can do the above to identify which chapters correspond with which episodes, except instead of having the "Title" option highlighted, have the "Chapter" option highlighted. Again, you're looking for a number format of #(current chapter)/#(total chapters). Once you have the chapter ranges for the episode, you can tell handbrake which chapter range to encode and encode all of the episodes to individual files.
Also, some DVD's have duplicate episodes for commentaries. Usually, these episodes will also contain the same audio tracks as the plain episode, so if you ever watch a show with the commentary track enabled, you'll want to make sure the audio track is present. If you aren't careful, you may end up encoding the same episode twice.
On another note, if you have an iPhone 4 or 4s, you can use the AppleTV 2 preset in iTunes to encode one file that'll play on the iPad, the iPhone 4, and look pretty good on a TV or computer screen too. Again, this is said assuming you'll be using handbrake for the encoding process.