Personally, I used the rip first with MTR and then encode with Handbrake method as well. The main reason being was that I could rip movie with MTR in about 20-30 minutes, but my iMac took about 3 hours to encode each movie. By using the 2-step method, I could rip about 5 or 6 movies each night after work, then set up my handbrake queue to encode overnight (TV preset + Two pass encode Turbo 1st pass) and those movies would be done about the time that I would get home from work the next day. Rinse & Repeat. Then I would tag the movies with MetaX, and put them on my external.
Just finished my 200 or so DVD library. Took about a month and a half. I had my wife's MacBook join the party most nights, so I could get more done. The frustrating times were when I would check on it in the morning and find that it crashed on the 1st encode sometime shortly after going to bed.