I have 3-4 polygons containing lots of lon/lat points. I want to identify to which polygon a specific point belongs. Any help in this matter is appreciated.
What you need is called a Spatial join. In Qgis, you can do this, by using the JOIN ATTRIBUTES BY LOCATION tool.
This is an tutorial which shows you how it can be done: http://maps.cga.harvard.edu/qgis/wkshop/join_spatial.php