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All those queries are generally filesorts and quite expensive. I would be very surprised if the query cache limit had much of an affect on anything performance wise.
@Bawolff: Does that mean you would be OK with increasing it to 2000 or are you suggestion some other course of action (like getting rid of the limits)?
I mean im ok with increasing. Some limit is probably needed, i just doubt 1000 vs 2000 would make any appreciable difference. I would go as far as to suggest 5000 to be reasonable.
Since cached special pages are paged via offset, a super really high limit would eventually introduce performance problems on the viewing cached results stage. But that's wiki agnostic anyways. No limits would probably also result in inserting a hundred thousand rows which would also be bad.
(i should be 100% clear that this is just my personal opinion. I definitely *do not* have the authority to decree what is and is not acceptable performance wise for wikimedia. I also have not profiled different settings or otherwise tested)