I know its crazy, but I rather like the plot of the GBA game--unlike so many video game conversions I like how the game actually worked as a synthesis of the manga and animes including the time-travel and the inclusion of the 60's ending that can then be 'remade' through time-travel (+ the aid of the phoenix) to redo certain things.
I can't pull out a particular story off the top of my head, but I do really love some of the manga stories that were more or less discrimination stories in disguise and the abuse that humans were laying on the robots. Here I think Tezuka uses Astro's status as a 'boy' to great effect, making him more sympathetic figure in a future world that cannot quite extend its humanity to robots.
Its far easier to name my least favorite (though I also can't think of any particular stories)--there's a fair number of these that are just grind and chug action adventure for the kiddies, and these I often feel miss the mark.
Oh god, that 80's episode where there are two Uran's...that's...the
ONE!
(best, cutest moment ever!)