If Rurouni Kenshin - Trust and Betrayal's OVAs count, that is definitely right up there too.
Mine is Serial Experiments Lain. I don't like that many shows from the 90s and before but that one definitely stands out to me the most among the bunch. If Rurouni Kenshin - Trust and Betrayal's OVAs count, that is definitely right up there too. If movies are counted, Perfect Blue too.