jQuery has smaller memory footprint than prototype (well depends on the use
case, but generally speaking, it is).
Their implementation is also different.

Mootools is also very light weight and flexible.  But jQuery has more
articles and books out there than Mootools, and it has quite some plugins as
well.

If you want to target iPhone, you probably want solutions specifically for
iPhone mobile safari/webkit, sine it's the most efficient.
But jQuery, with its ease of usage, certainly is a good choice.  And it's
also flexible if in the future you want to port your iPhone application to
other mobile browers, such as Opera Mini, Skyfire, touch mobile, android,
Nokia S60, etc.

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