These aren't really HTML5 video encoders but they do support the two currently competing encoding/compression formats - H.264 MP4 and Ogg Theora. With that in mind it means you could use them to encode your video to formats that work with the HTML 5 video tag. I have broken this list down into one, the other or both. Although I have not used all of these, I currently use the Any Video Converter free version as all I do at present is convert to .flv for my other site, Gamers Daily News. I do like it because I can set it up and then do batch conversions in the background while I work on something else.
Ogg Theora Video Encoding Tools
MiniCoder - MiniCoder is a batch encoder that tries to make encoding as simple as possible. It automatically encodes all audio tracks, checks for sub tracks and if supported by the container if fetches: Attachments and Chapters and puts them back into the output. Convert MKV, AVI, VOB, MP4, AVS, WMV to X264, Xvid, Theora. Requires external tools but has a built-in downloader(~24MB). FREE
ffmpeg2theora - A free, command line (Linux, Mac, Windows) theora converter.
GFrontEnd for ffmpeg2theora 2007.1 This is a simple frontend (GUI) for the ffmpeg2theora video converter, which converts videos to the OGG Theora video format Freeware
FFCoder- FFCoder is a .NET based audio/video converter, which is capable of transcoding audio and video files to various formats. It is a unified frontend for many freeware utilities such as FFmpeg, MPlayer and MEncoder. Supports 16 command line encoders : ffmpeg, mencoder, ffmpeg2theora, x264, xvid_encraw, avs2avi, lame, faac, Nero AAC, OggEnc, FLAC, Monkey's Audio, OptimFROG, Speex, MusePack and WavPack.Free
A great reference site for free Theora Tools - http://www.downv.com/Linux-software-download/theora-codec
H.264 MP4 Video Encoding Tools
Any Video Converter- It can convert almost all video formats including DivX, XviD, MOV, rm, rmvb, MPEG, VOB, WMV, AVI to MPEG-4, AVI, WMV, 3GP, 3G2 format for your iPod, PSP, iPhone, Archos, Creative Zen, iRiver and many other portable media players. It also supports any user defined video file formats as the output. Free Version of: Any Video Converter Pro - also a HD video converter which allows you to convert HD movies including HD AVI, HD MKV, HD WMV, AVCHD, TS, TP, MKV to videos playable on iPod, PSP and other devices. High definition output video size up to 1920x1080 are also available for MKV, AVI, WMV and MP4 output formats. You can extract audio from any video formats it supports to MP3, AAC, M4A, WMA, OGG and Wave.
Prism Video Converter Software - The latest version of Prism has been tested and will convert to AVI, WMV, ASF and Prism Plus will also convert to MPG, 3GP, MP4, MOV and FLV. Free Trial Available
Free Studio- With DVDVideoSoft freeware you can convert, edit and burn a lot of video and audio formats. Most key video formats are supported: AVI (DivX, XviD, etc.), DV AVI, MP4 (inc. Sony PSP, Apple iPod, Blackberry), WMV, 3GP, 3G2, QuickTime (MOV, QT), SWF, DVD, VOB, MPG, MPEG 1,2,4, DAT, VCD, SVCD, ASF, ASX, MJPEG, H.263, H.264, DVR-MS, FLV. Most key audio formats are supported: WAV, FLAC, APE, OGG, MP3, MP2, WMA, AAC, M4A, AMR. Free
Quick Media Converter - Supports flv, avi, divx, xvid, mpeg4, ipod, iphone, psp, 3GP, 3G2, AVI, DIVX, XVID, TS, DVD, VCD, MPEG, MPEG2, MP3, WAV, amr, m4a, mp4, vob, mov, h264, h263, wmv, wma. Also able to batch convert, crop and resize. Free (Donationware)
MPEG Streamclip - You can use MPEG Streamclip to: open and play most movie formats including MPEG files or transport streams; edit them with Cut, Copy, Paste, and Trim; set In/Out points and convert them into muxed or demuxed files, or export them to QuickTime, AVI, DV and MPEG-4 files with more than professional quality, so you can easily import them in a DVD authoring tool, and use them with many other applications or devices. Windows, Mac Free
H264enc - *NIX shell script - h264enc is a shell script which encodes video files or DVDs to the H.264 format using MEncoder. The script is targeted primarily at power users who like to tweak their settings in order to achieve best possible quality The script supports virtually all options of the libx264 library and has further support for 1-pass, 2-pass, 3-pass and fixed-quant encoding modes, 11 different software scalers, DVD cropping, interlaced encoding, deinterlacing of video content, setting output frame rate value, various audio codecs (MP2, MP3, AC3, AAC, PCM, ADPCM), file splitting, and more
Both OGG Theora and H.264 MP4 Video Encoding Tools
Super Converter - Input formats: 3gp, 3g2, amv, asf, avi, dat, dvr-ms, fli, flc, flv, m2ts, mpg, mkv, mov m4v, mp4, nsv, ogm, qt, rm(vb), str, swf, ts, trp, ty, ty+, tmf, viv, vob, wmv Output formats: Divx, DV Digital Video, FFV1, Flash Video, H.263, H.264, MPEG-I, MPEG-II, MPEG-4, XviD, WMV7, WMV8, WMV9, WVC1, Sorenson Video, Theora Free
HandBrake- MacOS X, Linux and Windows. Input: DVD source, DVD image or real DVD. Output: MP4, MKV, AVI or OGM, MPEG-4, H.264, Theora, AAC, MP3, Vorbis, AC-3. Free
Miro Video Converter (Mark thinks it's snazzy) - This free, Open Source project is part of the Participatory Culture Foundation who really need both an SEO person and a web person because they never showed up in a single Google search on the subject and their website isn't exactly bursting with info. You can convert a variety of formats to either MP4 or Ogg Theora with it but it doesn't explicitly say to H.264, just from. Mark assures me it can handle it.
Not surprisingly there are far more tools for converting to H.264 than there are for Theora. That's part of the argument against the codec as a standard for HTML 5 video. Plus, many of the tools for Theora are command line and without an easy-to-use graphic interface. However, development of new tools would certainly grow were it to be chosen and it would move out of the elite are of Linux and command line lovers and into the mainstream.
If you notice, most of the H.264 tools are free trial and then pay for full features.
This isn't a complete list, that would takes weeks to compile. If you've got a favorite tool that converts to H.264, Theora or both, drop a comment and let us know.