Welcome to the WP Hive forum!
Maybe this should be a thread unto itself? Anyway, I thought I might list a couple plugins I have had issues with.
1. Smart Update Pinger. The log file ends up in the wp-content/wp-hive folder (or, at least, that's what happened to me). Which means that file could get pretty massive as blogs are added.
2. Unique Article Wizard. Uses a config file to store settings rather than the WP database. I had to create a workaround to give individual blogs their own config files.
Interesting, and I agree - it's definitley a concern. Most developers don't write their code thinking that it might be used for multiple blog installations.
It would be nice to eventually have a published set of recommendations on how to develop a WP Hive compatible plugin.
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