AFAIK, no one has made a comprehensive list of games that have to rebuilt. In general, EA games and games with very high TOCs tend to require rebuilding.
Your better luck with trail and error or, if your lucky enough, browse the forums here and see if anyone has had problems rebuilding the same game you've tried to rebuild.
List of PlayStation 2 DVD-9 games
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This is a list of Sony PlayStation 2 games that use the DVD-9 (dual layer) format.
[edit] 0-9
* 50 Cent: Bulletproof (US)
* 24: The Game (EU)
[edit] A
* ATV Offroad Fury 4 (US)
[edit] C
* Champions of Norrath (US, EU)
[edit] F
* Forbidden Siren 2 (EU)
[edit] G
* Genji: Dawn of the Samurai (EU)
* God of War (US, EU)
* Gran Turismo 4 (US, EU, JP)
* Gran Turismo Concept: 2002 Tokyo-Geneva (JP)
* The Guy Game (US)
[edit] K
* Kessen 3 (US, GER)
[edit] M
* Madden NFL 2005 Collector's Edition (US)
* Metal Gear Solid 2: Substance (US, EU, JP)
* Medal of Honor: Rising Sun (JP)
* Midnight Club 3: DUB Edition Remix (US)
