Deciding where to put a flow control valve for a pond fountain or waterfall means taking a few factors into consideration. The actual filter part of a pond filter does not have a flow requirement, and so can always endure a decrease in water pressure. The pump that drives the water through the filter, however, can be damaged by running dry. A pond pump can run dry even when submerged if its intake is obstructed, or a valve is reducing the amount of water made available to it.
You always want to install the valve after the pump, on the output side. Installing a valve on the intake side can put added stress on the water pump and substantially reduce its lifespan. Pumps require constant water availability while they are running, and running them dry can quickly lead to overheating and burnout.
If you are looking to reduce the amount of water emanating from a fountain or waterfall by a slight amount, a ball valve after your filter is suitable. If, however, you find yourself turning the ball valve significantly to substantially reduce water flow, you may be putting additional stress on your pump by forcing it to pump into a pressurised output hose. Consider installing a "T" in place of the ball valve.
Placing a "T" with a valve immediately after your pond filter and pump can reduce the wear and tear on your pump and simultaneously reduce the output of your waterfall or fountain. A T-line can be installed with two hoses: one leading to your waterfall or fountain, and another draining directly back into the pump. This way, the pump can run at full capacity while your fountain or pump flows at the desired rate.
If the filter is separate from your pond pump, as with external biological filtration, you can safely place a ball valve before the filter as long as it is after your pump. The location of the pump relative to the ball valve is the important factor. When in doubt, place the valve after the filter, and reduce output by splitting the pipe, with one line going to the fountain or waterfall and the other returning to the pond.