I use MakeMKV to rip DVDs and Blu Rays to an archive format. I typically rip the main video title, the primary audio track, and all subtitles. I rip the videos to \\SERVER\Videos\Incoming, which is a share residing on my Windows Home Server. I have the script below running as a service (using SrvAny.exe and Any Service Installer), although running it as a service is totally optional. The script below watches that Incoming folder and when it finds a new file, it verifies that it's not still being written (that its size doesn't change in 5 seconds), and then it kicks off two transcode jobs using HandBrake, one for an iPhone and one for an archive format.
Once you get this job set up, all you have to do is rip your movie into \\SERVER\Videos\Incoming\[MOVIE NAME]\title00.mkv and the transcodes will be dumped into \\SERVER\Videos\Movies\[MOVIE NAME]\iPhone.m4v and Archive.mp4. In other words, one-click transcoding.