Now that you have everything installed, here's how to configure things as you go along with your first rip.
Open up DVD Decrypter. Go to Tools->Settings to change a few settings. Under the "File Mode" tab, set "File Splitting:" to "None" to make a single VOB file instead of multiple partial files. That way you can open the VOB with VLC media player to make sure it ripped properly before you begin converting it. Hit "OK" to save the changes and go back to the main screen. Under "Edit" hit "Select Main Movie Files" - this will give you an .ifo file and a .vob file, and that's all you need. It should leave out any trailers, etc. on the disc - so far, in my experience, it has worked. Now you can hit the picture along the bottom showing DVD->Hard drive and it'll start the ripping. It often takes around 10-15 minutes for me. You should be able to go into your C: drive and find a folder there with a folder containing this movie (if you used default settings.) Open up that .vob file with VLC to make sure it's alright. Especially check under Video->Subtitle Tracks for any subs and under Audio->Audio Tracks for any alternate languages (or commentary tracks.) Also spot check the movie, especially the beginning and the end, to make sure you have just the movie and nothing else. If you do have a little bit of extra, that can be trimmed in the end with AutoMKV so it's no big deal.
Start up meGUI. It can't go straight from a .vob file, you need to make a .d2v file. Fortunately, there's an easy-to-use tool to do that. Go to Tools->D2V Creator (Ctrl+2) and select your movie's .vob file under "Video Input" and it should pop up the audio tracks. If you don't want to keep any of them (particularly if there is a commentary track or if there is a Dolby 5.1 and a regular Stereo audio track in the same language) then deselect the check box next to that audio track. Make sure the "On completion load files" and "and close" checkboxes are checked (just makes things easier.) Now go under the "Queue" tab and find your D2V job queued up - hit "Start" in the bottom left. It'll pop up a progress bar but in my experience that bar never fills - don't worry, it does work. It often takes about 3 minutes or so. When it is done, it should load up the AVISynth Creator dialog box (which is why you had to install AVISynth first.)
Along with the AVISynth Creator box you should also have a "Video Preview" box of the movie file. If you have black bars across the top and bottom, slide the video along to a spot in the movie where the screen is fairly light so that it can easily tell what's movie and what's black bar. Then under ""Crop & Resize" hit the "Auto Crop" button. That should take out the black bar. Whether or not you have to crop (but especially if you do) it's good to resize to mod16. Hit the "Resize" checkbox and also the "Suggest Resolution (mod16)" box and it should fill in the 2nd number automatically. Check the "Appy auto Preview" and you should be able to see what your movie will look like when it's done.
Now for the filters - in that AVISynth script creator box, hit the "Filters" tab. As a general rule it's good to set the "Noise Filter" checkbox on (to the default of minimal) and you can leave the resize filter on "Lanczos (Sharp)" which is the default or I've also had good looks using "Bicubic (Neutral)" (only important to note if you have to resize.) Now comes a useful feature of meGUI - hit the "Analyze" button there on the right side a bit up from the middle. That will check to see if your movie is interlaced and such - if it's Anime or some other cartoon, be sure to check the "Source is Anime (isn't detected automatically)" box but otherwise it should just work. It'll take it a bit and it might have to scan twice, but then it'll autoset the filter settings. Once that is done, hit "Save" in the lower right and you're just about good to go.
Once the AVISynth window closes a new video preview window will pop up. Check that it looks good then close it - that's what your movie should look like when it's done. Now go back to the "Input" tab of meGUI and under "video" change the format from the default of MP4 over to MKV. If this is your first time, you'll need to set a video encoding profile. I've found that the best quality method (though it takes a while) is x264. I'd recommend "x264: Unrestricted 2pass Extra Quality" under "Encoder settings" to get good quality and still a good file size (probably around 800mb for the video part of the file.) It should also set up the audio track(s) down below. I recommend setting their encoding options to "Vorbis - Good (Q=4)" since it gives good results and it works well in the MKV format. If you have multiple audio tracks, don't forget to change this for each one (they'll be tabbed under "Track 1" "Track 2" etc.) When this is done, you can hit the "AutoEncode" button in the bottom right.
In the AutoEncode dialog box, you'll want to set it to "Average Bitrate" and change that to at least 1100, 1200 is even better. This number determines the overall quality. Below 1000 generally looks grainy. The trade off between size and quality makes rates higher than 1200 or so not really worthwhile. Now you're ready to hit "Queue" and you're almost done!
Go to the "Queue" tab of meGUI and check it over - you should have 1 audio process for each audio track and then you'll have 2 video processes (it's a two pass encoding.) The last process will be a 'mux' (putting the audio and video together.) Now you're ready to hit "Start" in the bottom left. Note that the initial progress bar that pops up doesn't really work but once it gets on to the audio encoding it should start giving a relatively reliable progress bar.
For me, this often takes around 12 hours in total. My longest rip took about 17 hours or so (but it was a super long movie.) I usually just let this run overnight.
When this is all done you should end up with a file called something like "VTS_02_1-muxed.mkv" in your movie folder (there on the C: drive by default.) Open this up and see if it works. If all went well you'll have audio and video that synced up. I've had this not work out a few times, and I'll write about cases like that in later posts. For now, you can be done if it works for you but if you want subtitles you'll need one more step.
In meGUI go to Tools->VOBSub and put your video file in under "Input" (I think it'll only accept the .ifo file.) It should load up the various subtitle tracks. Select them all, check the "and close" checkbox, and hit "Queue" then head to the "Queue" tab in meGUI and hit "Start" to run the process. You should end up with two files. Open the smaller one with Notepad. It should list a whole bunch of time codes and "filepos:" info - this tells the larger subtitle file when to display which part of the subtitles. Make sure that the time codes go all the way to the end of the movie (scroll down and check.) If you have multiple languages, it should go from one to another with a note about which language it is. If this is not right, if the timecodes don't go all the way to the end of the movie, then something got messed up. This has happened to me before. SubRip can be an option to try next. I have generally had better luck with this VOBSub than with SubRip. I might post later about special cases, but in general you should be set now.
Unfortunately, I've had little luck using meGUI muxing (combining audio, video, and subs) tools - I usually end up with subtitles on only the first half hour or so of the movie. This is where MKVMerge can come in.
Open up mkvmerge GUI and in the top box titled "Input files:" drag and drop in your muxed mkv file (from meGUI) and also the smaller of the two Subtitle files. This should put a video file, your audio files, and your VOBSub (subtitle) files in under "Tracks." It might not automatically detect languages, so select each track and edit the "Language:" part under "General track options" if needed. If you're lucky, all you have to do now is edit the "Output filename" down at the bottom (it'll default to the name of your muxed file, and "subs" at the end of the file name or something to make it different) then hit "Start muxing" and you should be in business. It usually takes around 1-2 minutes to mux. If all has gone well, you should now have an MKV file with audio tracks and subtitles
All this without any command line work