Scrapped Princess is the best example I know of. It’s a near perfectly told story, moving as it goes along from a small and simple story of three people traveling together to literal world-spanning drama, and ending with all of the threads neatly tied up.

Others that come to mind:

Cowboy Bebop

ODDTAXI

Vivy: Fluorite Eye’s Song

Akudama Drive

Heike Monogatari

Kokkoku