There is a lot of interest in my How to create MP4 files with multiple audio and subtitle tracks - which is a four-step process. I've learned a few things since then - so here is a new, simpler process and will cost you zero dollars.
I should stress that this is strictly for your personal use - which makes sense for me because I buy DVDs and put them in storage (simply because I don't have the shelf space). Buying discs, currently, is still the cheaper (and better value) than purchasing digital version, which are often more expensive or on par with its DVD version. I'm on limited/metered internet, so I can't waste my precious bandwidth to download gigabytes of data.
In order to start copying your DVD, you need to decrypt the disc. I think there is plenty of software out there to strip out the region coding or decryption of discs - but the one I've been using is DVDFab's Passkey Lite, which is free. This is only for DVD, if you want to do BluRay, you have to pay for the upgrade.
Handbrake is my choice for ripping DVDs. It's by far the slowest ripper I've ever used, but what it lacks in speed, it does make up for being free. There are some presets, but personally I've been ripping at the best quality that will run on the iPad. For Bluray, I find that the iPad will run at RF:20 at 1280x720p. For DVD, select "Strict" Anamorphic which keeps the original DVD size with little image quality loss.
As for subtitles and multiple audio, you have to add them on Handbrake's settings. Softcoded subtitles seems to only work on VLC or the iOS, which means that the subtitles won't work on PS3 or Xbox. If you want to hardcode subtitles, Handbrake does offer "Burn in" - but it only works if the DVD includes its own subtitles or closed captions. Handbrake won't burn in external SRT sources and it doesn't see BluRay subtitles at all.
Below are additional/optional steps to further enjoy your movies:
This step is unnecessary - but I still recommend it. I'm using MetaX to retrieve cover artwork and additional information (actors, release dates, synopsis,etc.)
I personally hate the VLC icons (it's like an "under construction" cones, it's UGLY and I sense that it's "beta"). The open source software VLC player will play all everything and offers audio and subtitle switching. If you want to watch movies on the television via a computer hookup, I found the interface for XBMC to be one of the best.
Most of my movies I store on a "NAS" (Network Attached Storage) harddrive. I have two and I love them both. Between the two, my Seagate GoFlex drive is my favorite, mostly because it's faster access and higher storage (3gb). 3GB is not enough for me (I own over 2,000 DVDs), but it should be big enough for most people.