I have different tablets Moto Xoom, Nook Color, iPad 2 & 3, Surface RT, and Samsung Slates. I also have LG BD390 and BD570 bluray players which can play some files across home network via shared folders on my windows PCs, and the LG's along with two of my Sony TV's also support DLNA (and I need to use a DLNA server like Serviio).
It gets a little complex to make backups of my DVD and Bluray movies to play on all these devices. There may be "better" ways to do this, but here is how I do it...
Currently I use the "alternate movie only" output option in BD-Rebuilder
(donate) in combination with AnydvdHD to rip my movies to my hard drive. It creates an MKV file with the main movie and selected audio tracks. I also specify 2-Pass with 8096 as the file size target to get me the best balance of quality and size. In most cases its hard to tell that it is not the original Bluray disc. BD-Rebuilder can keep all audio streams, or downmix if you want to.
Your post seems to indicate that you realize the optimum encoder settings for your playback device are key to making good looking files. And that is so true. But with all these devices and their different capabilities, how do you keep it straight?
I had no luck geting good looking video files using Handbrake and other tools, even with what was supposed to be "optimum" settings.
So for my tablets, I take that MKV BD-Rebuilder made and open it using DVDCatalyst
(pay for). It has been the BEST, Easiest, and most reliable way to give me great looking videos to take with me. I've used it to encode DVD's, Blurays, camcorder videos, etc. And they all look great. Ok, so DVD rips don't look as good as Bluray rips, but that is because of the DVD source. While it has specific profiles for MANY MANY devices (phones, tablets, PS3, WDTV, etc) I select the Motorola Xoom HQXT profile, but hit the "modify" button to change the max screen size to 1280x720 (default for Xoom is 1280x800). The resulting .MP4 files have been "portable" and play great on all my tablets (except the nook color which isn't powerful enough for it). Depending on device storage and how many movies you want to keep on it, you might need to need sacrifice quality for size and select a lower profile than HQXT (see -> http://www.tools4movies.com/video-device-profile-types-fast-hq-hqxt/
DVDCatalyst can also convert blurays to MP4, but I haven't found the best LOOKING profile to use for playback with my LG's and TV's, so while the Mp4's look good on a small screen (tablet/PC), they don't look as good on my 46 and 55 inch TVs. Additionally it converts or down mixes to 2 channel or 5.1 channel AAC. So I only use DVDCatalyst when it comes to making files for my mobile devices.
Keep in mind that using these tools can take from minutes to hours depending on your PC. For example, when I first tried using BD-Rebuilder, it took over 24hrs to compress a bluray to an ~8gig MKV on my 3.2Ghz P4. With my almost 5 year old Intel i7-860 (2.8ghz) it currently takes me about 1.5 to 2hrs. Newer PC's can be even faster.
Then we come to Subtitles. Some players can handle sub titles embedded in the video files, others can't. So I usually try to make .SRT files containing the subtitles. BUT usually I only do this for movies that have "forced" subtitles, like 2012, Avatar, John Carter, where there are subtitles only for the non-english speaking parts, because the process is pretty manual.