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79flavors

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. Supports WebM VP8 or VP9.

Though personally, for sheer compatibility's sake, I tend to stick to MP4 using x264 video and AAC audio.

I can't speak to "best"... but there are lots of quality settings you can tweak if you're unimpressed with the output quality.
 
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Rich

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The trick with not losing quality is usually being able to control the target bitrate for the output - many packages default to a bitrate that's too low.

If the package 79flavors suggests doesn't work for you, another you can look at is VirtualDub. Haven't used it in a while, so I'm not 100% sure if it supports webm as an output format, but it definitely lets you fiddle with knobs like bitrate.
 
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79flavors

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Handbrake has two options for bitrate, at least when using MP4/x264 (probably the rest too, but I can't speak to that).

It can output Constant BitRate (CBR), with the bitrate fixed and explicitly specified.

Or you can use Variable BitRate (VBR) which you can either pick a "Constant Quality" setting (which scales logarithmicly between 50-Low Quality and 0-Lossless) or a "Average Bitrate", where you pick a number and the VBR fluctuates up and down depending on the image composition.

VBR results in a smaller file size.

I tend to use CQ=20 for everyday image quality and 18 for stuff where image quality matters more to me than filesize. It really comes down to how much "flat color" space is within your video (large areas of black sky or pale blue wallpaper for example). And then, obviously, you can't increase the image quality beyond that of the original source. The higher the CQ number, the more those flat areas are going to fragment and be painfully obvious.

The other reason I like Handbrake though is that it includes options to optimize for streaming video. Organizing the frames so they load contiguously and buffer better. Whilst I don't stream the resulting videos, I have noticed the player I use tends to buffer larger blocks beyond the current play point. I could be purely wishful thinking on my part, but it gives me a warm fuzzy feeling knowing that option is switched on for media I've recoded.
 
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