In terms of quality, compression, functionality, and ease of use or any combination of the above.
I'm not an expert on encoding, I just know how to play with basic settings like bit-rates with multi-pass encoding and I have close to no idea how to use filters or command lines.
I've been using mediacoder, minicoder and vidcoder,
mediacoder works well in terms of options and functions and I've learned to become used to it in terms of ease of use although the quality isn't always the best.
I like minicoder because it's very strict when it comes to sizes and bitrates and the quality is generally good but sometimes it lacks flexibility and I get errors without explanation sometimes.
As for vidcoder well I havn't used it as much but it doesn't seem to be able to reliably control sizes and bitrates and the quality is dubious despite what appears to be a good range of organized functions.
So given all of that what would you guys recommend?
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For a balance of power and ease of use I don't think you can top handbrake or vidcoder. They're the same encoder with different GUIs really. I don't agree the quality is bad. You're probably using bad settings.
Many of the really good, powerful encoders recommended here by the more serious video geeks are not suitable for beginners.