Hi. I'm using the following settings for Non-HD. HD is similar but wider format
Compression: H.264
Quality: High
Frame rate: 24
Key frames: Automatic
Frame reordering: no
Encoding mode:Best quality multi-pass
Data Rate: Automatic
Dimensions: 800x 600
Sound...
Format Integer: (Little Endian)
Sample Rate: 12k, Mono
Render quality: normal
Wow, you're killing your audio quality for very little gain. Don't worry about that as much as video.
Also since viewing from your website is your goal, you want to do things that accentuate streaming. It will end up with a large file, but it will be playable faster to the viewer so it will "look" like it downloads faster.
Try this and see if it doesn't give you better results for HD
Do this thought Quicktime Pro...
Video:
Compression: H.264
Frame rate: 24
Key frames: every 120 frames
Frame reordering: yes
Encoding: Best Quality ( multi pass )
Data Rate: Restrict to: 5000 kbits/sec
Dimensions: 800x450
Optimize for: Streaming
Sound:
Format : AAC
Channels: Mono
Rate: 44Khz
Show Advanced settings ( checked )
Render settings: Best
MPEG4 AAC LC Encoder Settings:
Encoding strategy: Variable Bit rate Constrained
Bit rate range: 32-36 kbps
( and back on the quicktime menu.... )
Prepare for Internet streaming: ( checked )
Fast Start Compressed Header
I set your resolution lower that you probably are used to here and the data rate is likely too high... do a test encode of a 30 second-1 minute clip and see how it looks at 5000kbit and then step it down to 4000... if it looks to bad, bring it back up to 4500, and continue until you find the sweet spot for your footage.
Hope this helps! ( and gives you good results! )