Just following up with an update on this:
Our system was crashing due to out of memory errors when users were running large reports.
PTC Tech Support say that there are no other limits that can be set other than wt.pom.queryLimit to prevent large reports crashing the Methodservers (Seems like a massive oversight to me).
We have hence had to set wt.pom.queryLimit to 200000 as a compromise between large reports crashing the system but having the value large enough such that it does not damage the legitimate internal DB queries of Windchill.
An SPR has been raised against R&D in order to add a reporting querylimit property, but this will not be available to us in Windchill 9.1 and will hopefully appear in a later release of 10.0 or 10.1
There is one other sort of work around to prevent large reports crashing the system and that is to add an attribute to the end of the url of the report to set the query limit for that particular report, something like this:
This can be manually added at the end of the report URL prior executing it for testing purposes.
Regards
Gary