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I would choose "Each site has it's own database" for these reasons:
1) Less data for the MySQL engine to have to sift through to compose a page, thereby increasing maximum load speed.
2) If customizations are made to a specific site, one does not necessarily have to consider the effect on any other site.
3) Sites which do not store data that is used in other sites would have blank data in the table, thereby wasting space with virtually no gain.
4) Data which is used for statistical calculations could be stored in a table with the same structure so that data could be exported from the live server, recomposed on a data mining server, and then queried using MERGE table so that data mining does not impact the live server and during the data mining process, only necessary data is parsed.
5) If you have to move one site to another server (due to excessive bandwidth usage, for example), then such move does not need to consider the other sites and unnecessary data does not also have to be moved in order to maintain your functional structure.
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Jeremy Miller
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