Use Handbrake. When you put in the dvd it will recognise each episode as a title, and you can use the queueing function to encode each episode separately. You'll recognise the episodes from the rest by the duration of them.
There's a lot of discussion on the best quality/file size trade-off, so the best thing you can do is try different settings and play them on the player you want, and work with the settings you're happy with.