from IGN.com
Sony may have included the PS2's CPU and GPU with every PlayStation 3 system, but the system still appears to be having some problems with backwards compatibility.
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We did find a few problem titles by looking through the list. Here's a quick run down.
# Tekken 5: A number of modes don't play background music properly.
# Xenosaga Episode II: The opening movie sometimes stops and sometimes doesn't properly play background music.
# Code Age Commanders: Problems (including data loss) with save game data.
# Radiata Stories: Background music during movie scenes may not play back properly.
# Star Ocean Till the End of Time (includes Directors Cut): Movie scenes may not have proper sound playback.
# Driving Emotion Type-S: BGM may not properly play back during races
# Gran Turismo 4: The screen may freeze following the title demo.
# Hot Shots Golf 3/4: Some sort of problem with the controls becoming unresponsive
# Operator's Side: The game freezes at the logo screen when started up with the Seamic controller
# Onimusha Dawn of Dreams: Screen will occasionally appear 2cm to the right
# Hyper Street Fighter II Anniversary Edition: The screen will not appear correctly in some instances. The S.F.II Movie cannot play properly.
# Megaman X7: There are times when the background music won't play properly
# Devil May Cry: The screen will sometimes freeze during the title demo
# Onimusha: During movie playback, the sound will occasionally stop
# Suikoden III: Cannot read PS1 data during the game.
# Silent Hill 2: When going from the title screen to the demo screen, the screen may freeze
These are the major problems we found looking through the numerous pages for Sega, Namco, Capcom, Square Enix, Sony and Konami.
Some problems, including those for Ace Combat 5, Oz, SOCOM and so forth, were fixed with the System 1.10 update. Sony still lists those problems in the database.
We also noticed a few recurring problems, sometimes based off a common feature, sometimes carried across an entire series of titles. The PS3 Virtual Memory Card specifications do not allow for PS2 games to read PS1 data, which is something that's apparently used in Suikoden III and a few other titles. Most of the microphone-compatible games seem to have problems. Konami's dance/music games seem to have a number of problems.
In addition to the software compatibility issues, Sony has made public the issues that arise due to hardware differences between the platforms, specifically the PS3 not using physical memory cards, not using a multitap, not having rumble built into its controller and other issues related to different hard disk and USB specifications.
As previously announced, you can keep using your PS2 game saves by purchasing a Memory Card Adapter (which is currently harder to find in Japan than actual PS3 units, it seems). Once you have the adapter, you'll be able to transfer your save files to the PS3 hard disk. The only catch is that games whose save icon displays a "No Copy" icon in the PS2 browser cannot have their data copied over.
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HDMI also gives problems to PS2 games. Sony states that as of 11/11, when the PS3 is connected to your entertainment center using HDMI, PS2 and PS1 games will output only in 2ch digital. When switching to Dolby/DTS modes for PS1 and PS2 games that are compatible with these sound systems, you'll get no sound output. For now, Sony recommends using an optical cable for such titles. This, of course, will require that you go into the settings menu and change the audio output cable.
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Games that use the hard disk will currently not run. The problem is that the built-in PS3 hard disk cannot currently be used as a PS2 hard disk. We haven't tried it out ourselves, but this means games like Final Fantasy XI and Nobunaga's Ambition Online won't work.
The complete article here: http://ps3.ign.com/articles/745/745439p1.html