Joe fixed most of these a while back, but I recently encountered one he missed - Resource import. We should search for any remaining instances that need to be fixed. There are two ways to look for these: 1) grep through the code base looking for them 2) try to do various actions on 1000 or more items via the GUI of the perf environment, which contains 1000s of Resources, looking for ones that bomb I think there will be many queries with IN clauses in the code base that would never be passed more than 1000 items in a realistic use case, so I think 2) will be an better way to find the important ones that need to be fixed.
Closing this. This will eventually fall out of perf testing. Specific instances should be tracked in specific BZs.
Reopening this, since its a tracker bug. Actually added the keyword this time. The specific instances of this problem which jay mentions are listed in the Depends On field of this bug.