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For most phones I use Super C. It's fast to convert and is compatible with more input formats than Handbrake.
Download link is at the bottom on their page.

For the Palm Pre I use Videora

Xperia X1 Encoding:
Video Encoding GUI
You could use CorePlayer and not require encoding, but the advantage to this is that WMP is hardware accelerated and CorePlayer is not.
Also you may get reduced filesize from the encoding.