In Champions League knockout stages , if the second leg match is tied in normal time on aggregate then in extra time if both score a goal each , will it go to penalties or is it based on home away goal rule?

X wins, on the away goals rule. Extra time is not to be considered as a special circumstance, but just an extension of normal time to facilitate a result. Edit-  found the following on wiki: "There has been at least one case of a wrong application of the away goals rule by a referee in an international club tournament. It happened in a second-round tie in the 1971–72 European Cup Winners' Cup between Rangers and Sporting Clube de Portugal. This fixture had the following scorelines: First leg: Rangers 3 – 2 Sporting Second leg, after 90 minutes: Sporting 3 – 2 Rangers Second leg, after extra time: Sporting 4 – 3 Rangers Since the teams were now level 6–6 on aggregate, the Dutch referee Laurens van Raavens ordered a penalty shootout, which Sporting won 3–0. Rangers appealed the loss, however, on the grounds that Van Raavens should not have ordered the shootout, since the Rangers goal in extra time in Lisbon gave them a lead of three away goals to two. Rangers won the appeal and went on to win the Cup Winners' Cup that season." FIFA, UEFA CL and Europa follow the above ruling for two-legged knockouts, whereas CONCACAF and AFC do not, i.e., the away goals rule applies at the end of normal time, but if an equal no. of goals are scored in Extra Time, the game goes to penalties

X wins on away goals rule. See here - http://en.wikipedia.org/wiki/Away_goals_rule#Summary The away goals rule condition is checked even after extra time for Champions League, Europa League and FIFA World Cup qualification. Whereas, CONCACAF Champions League, AFC Cup and AFC Champions League, check for away goals that were scored within the first 90 minutes. One could argue that X had more time for scoring an away goal. But Y got more time to play on home ground(home advantage).