I could name a few vns which had bitter-sweet endings - G-Senjou, Cross Channel, Chaos;Head.
Some prime example in animes would be Angel Beats, Gurren Lagann, FLCL, Kara no Kyoukai, Code Geass, Fate/Zero.
Simply put bitter-sweet endings are the ones in which the end goal was achieved but the characters had to make a lot of sacrifices for it, which results in leaving both a sad feeling and a feeling of happiness.
Note: Being the heartless person I am, some of my bitter-sweet ends are considered as bad ends by some people.