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The following article explains how to customise the file types that can be compressed in IIS 6:

Customizing the File Types IIS Compresses (IIS 6.0) [MS TechNet]

The metabase settings discussed are global settings.

Can I configure this on a per-site basis?

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Yes, you can.

See "To enable HTTP Compression for Individual Sites and Site Elements" here.

Edit: I misread the details of the question. I am pretty sure I have configured different file extensions for compression on different sites in the past, but I also can't seem to find any definitive answer right now. I'll check when I'm at work tomorrow.

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I read that. That's just the settings to turn on/off compression by site. There's no mention about whether you can customise the file types on a site by site basis. – Kev May 19 '10 at 9:35
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After some digging about it looks like this is a global setting and can only be configured at the following metabase location:

/LM/W3SVC/Filters/Compression/gzip
/LM/W3SVC/Filters/Compression/deflate

For more info:

HcFileExtensions - MSDN Library

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