DVD shrink's pretty nice. Not only can you remove parts you don't want, but if you can wait a few hours, you can compress the parts you do want so they will fit on a DVD. I backed up my Matrix DVD using DVD shrink and I told it to really compress the menus and compress the actual movie as little as possible. It looks far better than the best DivX movie on the internet. I highly recommend it.
I personally use it in combination with DVD decryptor, but I've been having problems with skipping DVDs lately, but that may be unrelated to the software I'm using. I haven't had the time to try to narrow it down, but when it works for me, it works real nice.