As far as I am aware, the iPhone doesn't use the use the same Youtube that you are using on the N900, instead it's a specially adapted Youtube approved by Apple. Because they simply won't allow you to go to the full Youtube site like you can on your N900. But I may be wrong (but I'm pretty sure I'm not).
The N900's Media Player leaves a lot to be desired for it's video capabilities. And I can certainly say I get mixed results from Youtube.com.

Try installing "Cutetube-QML", "KMPlayer" and "Tweakflash plugin" from the catalogues, as suggested by the other guys.