When you are playing them inside a keynote presentation, you're layering two sets of load on the GPU for both display/transitional effects in keynote, along with the video itself. Keynote itself is relatively new, and HD video in keynote is very likely a rather "bleeding edge" type deployment. Apple (understandably) develops applications with the "average" user in mind. Up until this year, nobody was really even considering HD video. Lately, with the advent of 1080p projection units (wow, big $$$ there, 10k+ for a good 1080p unit) HD video is starting to take off, but it'll be a while yet before it's mainstream. I imagine they are working on optimizing quicktime for HD playback, but as of yet I do not believe HD video decoding is accelerated on the current crop of notebook video cards in Apple machines, and this is why you're experiencing problems. If you were to play uncompressed HD movies, and had an external RAID providing the bandwidth required for this, I imagine you'd have no problem.
Right now you are limited by CPU in terms of HD video playback. Launch a HD video inside keynote, then fire up activity monitor. You'll see your CPU is heavily stressed. Until Apple puts video cards in their notebooks that can do h.264 decoding as well as improve quicktime to support hardware decoding for h.264 streams, you're not going to see a whole lot of improvement. The Merom update isn't going to give you enough cpu horsepower to see a noticible difference. The Santa Rose upgrade might, however, be enough. Hopefully we'll have hardware decoding for h.264 across the board by then, and your issues will be resolved.
Cheers,
David