There are so many... a really hard decision, but here JUST A FEW of my top-favs:
Assassin (join the resistance week) intro and outro - out of this world!!!
Dead Star (V-Festival 08) love the lyrics so much and the crowd-singing is perfect!!!
KoC (Wembley 07) when the riff kicks in ("c'mon Wembley") OMFG!!!
Muscle Museum (Glasto 04) at 0:59-1:13 Matt is just unbelievable!!!
Showbiz (Reading 06) The scream/falsetto at the end is so amazing and I love Chris' headbanging!!!
MotP (Abbey Road/5:44) Around 3:13 love it so much, when Matt, Dom and Chris look at each other, you can really feel, how close they are!!!
Fury (RAH 08) at 0:23 and 3:35 look at Matt our guitar-god!!!
Citizen erased (BDO Sydney 04) So raw... and look at Matt's face, when he is playing the main-riff!!!
Endlessly (04) Beautiful song and lyrics, the tear in Matt's eye at 3:20 makes me cry!!!
... I could go on and on... because I L O V E all Muse-Songs especially the live-versions!!!