I dunno best way, but my method: export uncompressed mov file (OS X) with alpha channel,
then add background and convert to gif in CS3/4, or convert to flash in visualhub.

however, I feel that anim gif is obsolete, excepting things like avatar on left (8, 16, 32 colour). 
they allow flash in these forum posts but they discourage it, for obv. reasons.
swf/flv is much smoother and smaller file size for mega-colour anims IMVHO. 
one of ipad's downsides: they didn't add flash to the models distrib. at wednesday's conf.
with jobs as keynote speaker, but that's just a matter of time, as it's web standard now,
just like gif useta be 15 yrs ago.