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What's the most compatible configuration for low system specs as far as all games go? That is, if you were going to start with one config to run the most games at reasonable speeds what would it be.

I'd start with default settings+enabling the recommended speedhacks.

Most settings will depend on the specific game and your specs anyway.

One thing that can make a considerable difference is setting the VU Cycle Stealing up one step as well. Some games won't respond well to the addition of VU stealing, but some games need it to run full speed (even at 4.9Ghz).