Thanks everyone. I'll sit tight and let the product evolve for a while and revisit this question in the future.
I've used Handbrake a lot and I've also tested out CloneBD.
BDs tested:
- Gladiator
- Se7en
- Looper
- Heat
Movie procedure before CloneBD: Copy+paste the largest m2ts file (movie) to a folder of my choosing -> Encode with Handbrake.
- Preview clips: CloneBD lets you see frames from different m2ts files on your blu-ray. This is nice because it is easier to see which clip/file you want. (If you want another video file then the main movie). Handbrake only list the files along with the time code.
Winner: CloneBD
- Audio: Handbrake allows you to specify exactly which audio tracks you want with either a pass-through option or encode option. BDClone only lets you select "language type" of audio tracks, which is a problem. This is because there can be several "English" tracks, but those are commentaries and not the original soundtrack. There are limited options for what you can do with different audio tracks, unlike Handbrake.
Winner: Handbrake
- Subtitles: Subtitles are handled in a different way than they are on a regular DvD. One BD might have 10-15 different subtitles and this causes a problem for Handbrake. At the time of writing, Handbrake might show all subtitles as "1.Unknown, 2.Unknown" etc, so you need to manually figure out which number your subtitle is/are. I've not encountered any issues with CloneBD and it shows up as "English, Danish, Norwegian, Swedish" etc.
Winner: CloneBD
- "Segments": Sometimes the BD contains lots of different m2ts files that makes one movie (Gladiator), other times it is just one single file for one movie. CloneBD crashes every time I try to either store the Gladiator movie in .mkv/.mp4 format or with the original blu-ray structure. In order for Handbrake to encode the video you need to let Handbrake inspect the blu-ray first. Then Handbrake will find "playlists" and you choose the time code that fits you. (Gladiator contained both theatrical and extended cut).
Winner: Handbrake!
Note1: After I wrote my initial thoughts about the audio, I noticed that you can remove unnecessary audio tracks with the setting pop-up on the right side of each video clip. So CloneBD will do the same for me as CloneDvD did, copy only the information I want to disk. Then I'll fine tune the encoding for the final result with Handbrake. Handbrake also supports x265, so there is that... but I'll use x264 for now.
Note2: If you want CloneBD to copy/encode the video directly to a .mp4/.mkv, you seem to only be able choose between AAC and AC3. For some reason you can't get DTS-HD, which I find a bit strange. Correct me if I'm wrong here!
Note3: When I told CloneBD to make a BD structure with select video files (Se7en, main movie file only), the stream folder also contained the following files: 00065.m2ts, 00066.m2ts, 00067.m2ts, 99001.m2ts. The main movie was named 00020.m2ts. The other files ranged from 100KB to 11MB in size which isn't a huge problem, but made me curious as to why they show up. I didn't select those files.
Note4: The problem with the Gladiator movie still exist. I believe that might be an issue for all BDs that contain both the theatrical cut and an extended version.
Conclusion:
It saves you a lot of hassle in regards to subtitles and if you need a physical copy on a 25GB disc. Handbrake does not allow you to estimate a size for the end result, only a constant bit rate or constant quality.
If you do not have the money/want to save money, you can always use MKVmerge to extract the video, audio and subtitle tracks you need. With "Mediainfo" you can "easily" see which audio/video tracks you need by looking at the details and its corresponding ID. It is way harder for subtitles though since a lot of them are named "unknown" and they are still named "unknown" in media players like VLC.
For the average Joe, this is a great all-in-one solution to get compatible videos for your media device. If you want to nit-pick encoding details, then Handbrake is the option for you.