> Here are my Mplayer benchmark results for .webm file (1792x1080): [...]
> what is more interesting, for a mp4 file (1280x544) results are: [...]
> so a big advantage for the PCIe models over the AGP equipped G5.

Per-clock performance (higher = better) normalized to "1.00 = slowest" is this:

webm | mp4
1.33 | 1.86 : PowerMac G5 "Quad"
1.00 | 1.00 : PowerMac G5 "DP"
1.22 | 1.61 : iMac G5
1.25 | 1.07 : PowerBook G4
1.28 | 1.12 : iBook G4

(I hope I correctly assume that the video files were read from the RAM disk in any case, so that storage connection speed plays no role.)

Your observation is certainly correct as in both tests, the slowest is the AGP G5 and the fastest is one of the PCIe G5s, so among the G5s the type of GPU connection seems to be the determining factor for video playing performance.
Regarding G4 vs. G5, it can be seen that the G4s are found between the two PCIe G5s for high-res WebM video replay, and that the G4s are found between the AGP G5 and the PCIe G5 (but just above the AGP G5) for low-res MP4 video replay. I'd say that there can't be a unidimensional explanation for these G4 vs. G5 per-clock performance results. It's rather that these mixed results stem from factors like SIMD performance, memory bandwidth and microarchitectural code tuning interfering with each other.