Going on the ones i actually watched, i picked:
98-99 - All the the KO stage games were pretty entertaining and quite balanced apart from the Bayern - Kaiserslautern game. Final was very dramatic and the group stage back then always proved to be interesting with only 6 teams qualifying. Man Utd - Barca and Inter - Real were some great games.
00-01 - Entertaining set of KO games on the whole. Was good seeing Real - Bayern back in those days. Both group stages had some good matches - Lazio - Real Madrid, Juventus - HSV, Milan - Barca, Bayern - Arsenal etc.
04-05 - Obviously a classic final. Milan - PSV semi final ws very good and Chelsea - Liverpool had some good controversy. Barca - Chelsea in the last 16 was also a classic, plus the group stages had some good matches like Milan - Barca and Liverpool - Olmypiakos.