I can't find the "Points in Polygon" command under the vector-analysis tools. It is missing from the pull down menu. Any ideas why? I just loaded QGIS for the first time on my new PC.
This command from FTOOLS is now in the processing panel. Check in the QGIS geoalgorithms folder. I suppose what your are looking for is "Count points in polygon" ? If it doesn't look like mine, check also if "advanced interface" is selected in the dropdown list at the lower part of the panel.
If you can't find this panel, go to Plugins and check if Processing is checked
You can add it inside a button with the Customize Toolbar Plugin :
You'll have it in a toolbar :