ArcGIS Proxy Server and Layer Queries
If you are using ArcGIS Server and need to set up a proxy server for large (i.e. greater than 2k) layer queries, you need to make sure that you install the proxy server on the application server as opposed to the ArcGIS Server. If you don't, you'll get no features returned even when it is patently obvious that features should be returned for that query.
One of the odd symptoms was an OPTION command in firebug for the query request instead of a POST as one would expect. It turns out that this indicated a cross-domain AJAX query (the request was made to see what options were available from the server but, since it was a cross-domain request, it never got there) which is a no-no.
I spent several wasted hours trying to figure this out. Thanks to the hints at http://stackoverflow.com/questions/1478622/firebug-net-monitor-options I was able to resolve this issue and move on.