Sorry for the belated response and thanks for the replies.
What I was trying to convert is my Ren and Stimpy DVDs. I ripped them a few years ago to PC with the free version of WinX DVD Ripper. Output was/is AVI.
Now in particular, I was looking at the handbrake converted output in the Black Hole episode (to Apple3 preset). There are some transitions, and the animation looked horrible. I believe this is more due to the source then the conversion. This was a very early episode.
I tried reconverting it 3 times, with Universal settings:
Universal Default
Universal Decomb Default On
Universal Deinterlace Default On
In all cases, the source looked pretty appalling at the part I was checking, this is 2 minutes in after they get pulled through the black hole. No matter the conversion, that scene looked horrible. I then skipped forward to a few other spots, and what I see isnt nearly as bad.
If I look at the same scene, using the unconverted AVI in VLC, its just as brutal at that 2 minute point.
So my conclusion is this is a source issue.
I will try a one pass rip/convert with Mac DVD Ripper pro, and see if I get better results.
I will also skip to one of the later season episodes, and see how that converts.
FYI I am not using the CLI with Handbrake, just the GUI/main app, and almost always not touching anything other than the presets. Given some other searches on Handbrake and animation, I read about Decomb/Deinterlace/Detelecine and as described above, made some changes in the Picture Settings to experiment. Otherwise I have been just selecting a preset, adding items to the queue and letting it do its work.
I have noticed the PC version will go insane with memory after a period of time, so I have been telling it to shut down after each batch.
So that about covers the animation.
Now, I also have some older 70s era DVDs. For example, Jerry Anderson's UFO series.
With older material like that, is it worth the space/size to use the Apple3TV presets?
I have seen some people arguing in places that the Universal setting is a solid default to use, and it wont produce files as large as the Apple and the quality difference is non-existent with more limited source.
Thoughts? And again, I'll do some more reading..
I upgraded my Mac Mini to Mountain Lion and as a result had to get Caffeine to keep Handbrake running unattended.
Other than that I have been reading the sticky at the top here, regarding automating the process.