I have put together CM Punk's WWE PPV History (See Below). I do not count his time in ECW as WWE. I started from when he won his first Money in the Bank match, which is basically when he really started his WWE career, even though he did stay on ECW for a few more months.
So out of all his PPV matches I would say my favorites have been basically anything with Rey Mysterio.
I liked his Wrestle Mania XXVII match with Randy Orton
But my favorite match of CM Punk's in the WWE has to be his T.L.C. Match with Jeff Hardy
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Capitol Punishment (6.19.11) CM Punk defeated Rey Mysterio
Over The Limit (5.22.11)The Big Show and Kane defeated The New Nexus (CM Punk & Mason Ryan)
Extreme Rules (5.1.11)Randy Orton defeated CM Punk in a Last Man Standing Match
WrestleMania XXVII (4.3.11)Randy Orton defeated CM Punk
Elimination Chamber (2.20.11)John Cena defeated CM Punk, John Morrison, Sheamus, Randy Orton, and R-Truth in an Elimination Chamber Match for a WWE Championship Match at WrestleMania XXVII
Royal Rumble (1.30.11)Alberto De Rio wins Royal Rumble Match (CM Punk entered #1, was 21st Eliminated, 7 Eliminations, 35:21 Time in Rumble)
TLC (12.19.10)
Survivor Series (11.21.10)
Bragging Rights (10.24.10) Team Smack Down defeats Team Raw in Bragging Rights Match (CM Punk of Team Raw was 10th Superstar eliminated 24:07 into the match
Hell in a Cell (10.3.10)
Night of Champions (9.19.10) The Big Show defeated CM Punk
Summer Slam (8.15.10) The Big Show defeated The Straight Edge Society (CM Punk, Joey Mercury, and Luke Gallows)
Money in the Bank (7.18.10)
Fatal 4-Way (6.20.10)Rey Mysterio defeated Jack Swagger (C), CM Punk, and The Big Show for the World Heavyweight Championship
Over the Limit (5.23.10) Rey Mysterio defeated CM Punk in a SES Pledge vs. Hair match
Extreme Rules (4.25.10) CM Punk defeated Rey Mysterio, if CM Punk lost he would have had to Shave his head
WrestleMania XXVI (3.28.10) Rey Mysterio defeated CM Punk
Elimination Chamber (2.21.10) Chris Jericho defeated The Undertaker (C), John Morrison, R-Truth, CM Punk, and Rey Mysterio in an Elimination Chamber Match for the World Heavyweight Championship
Royal Rumble (1.31.10) Edge won Royal Rumble Match (CM Punk entered Rumble 3rd, was 7th Eliminated, 5 Eliminations, 10:04 Time in Rumble
TLC (12.13.09)
Survivor Series (11.22.09) Team Kingston defeated Team Orton (CM Punk was on Team Orton)
Bragging Rights (10.25.09) The Undertaker (C) defeated CM Punk, Rey Mysterio, and Batista in a Fatal 4 Way Match for the World Heavyweight Championship
Hell In A Cell (10.4.09) The Undertaker defeated CMP Punk (C) in a Hell in a Cell match for the World Heavyweight Championship
Breaking Point (9.13.09) CM Punk (C) defeated The Undertaker in a Submission Match for the World Heavyweight Championship
Summer Slam (8.23.09) CM Punk defeated Jeff Hardy (C) in a T.L.C. Match for the World Heavyweight Championship
Night of Champions (7.26.09) Jeff Hardy defeated CM Punk (C) in a Singles Match for the World Heavyweight Championship
The Bash (6.28.09) Jeff Hardy defeated CM Punk (C) by DQ in a Singles Match for the World Heavyweight Championship
Extreme Rules (6.7.09) CM Punk defeated Umaga in a Samoan Strap Match
CM Punk defeated Jeff Hardy (Cashed in Money in the Bank right after Hardy won the title from Edge) in a Singles Match for the World Heavyweight Championship
Judgment Day (5.17.09)Umaga defeated CM Punk
Backlash (4.26.09) Kane defeated CM Punk
WrestleMania XXV (4.5.09) CM Punk defeated Kane, Mark Henry, MVP, Shelton Benjamin, Kofi Kingston, Christian, and Finlay in a Money in the Bank Ladder Match
No Way Out (2.15.09)
Royal Rumble (1.25.09) Randy Orton won the Royal Rumble (CM Punk entered 18th, eliminated 18th, 1 Elimination, 22:29 Time in Rumble
Armageddon (12.14.08) CM Punk defeated Rey Mysterio in a Number One Contenders Match for the WWE Intercontinental Championship
Survivor Series (11.23.08) Team Orton defeated Team Batista (CM Punk was on Team Batista)
Cyber Sunday (10.26.08)
No Mercy (10.5.08)
Unforgiven (9.7.08) CM Punk vacated/stripped World Heavyweight Championship after being punted by Randy Orton in a backstage segment
Summer Slam (8.17.08) CM Punk (C) defeated JBL in a Singles Match for the World Heavyweight Championship
The Great American Bash (7.20.08) CM Punk (C) fought Batista to a double DQ in a Singles Match for the World Heavyweight Championship
Night of Champions (6.29.08)
One Night Stand (6.1.08) The Big Show defeated CM Punk, John Morrison, Tommy Dreamer, and Chavo Guerrero in a Singapore Cane Match for an ECW Championship Match against Kane at Night of Champions
Judgment Day (5.18.08) John Morrison and The Miz (C) defeated Kane and CM Punk in a Tag Team Match for the WWE Tag Team Championship
Backlash (4.27.08)
WrestleMania XXIV (3.30.08) CM Punk defeated Shelton Benjamin, Chris Jericho, Carlito, MVP, Mr. Kennedy, and John Morrison in a Money in the Bank Ladder Match