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Keep in mind that x264's defaults have quite a few psy optimizations that dramatically decrease PSNR, since by default x264 optimizes for your eyes, not the benchmarks.

This now applies somewhat to Theora as well (in current SVN); they ported over a similar optimization to x264's Variance Adaptive Quantization, which dramatically increases SSIM but lowers PSNR.

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I noticed too, that H.264 has some special threatment to improve encoding of uniform regions which frequently occur in artificial images.

Regardless of what video codec you use, the rate-distortion greatly depends on the encoder software and how you use it. When you use MEncoder's x264-compression for example you can tell it to do multi-pass encoding, more accurate motion estimation, use less keyframes, more frames for pixel prediction, ... . Many people don't even use multipass encoding when they convert their videos.

Update: Here's an interesting website about work on the theora encoder http://web.mit.edu/xiphmont/Public/theora/demo8.html

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