The "Pour Over Same Net Objects" is the typical selection. This will result in the polygon connecting (typically by thermal reliefs) to all objects on the layer that have the same net within the perimeter of the polygon. This would include all same-net objects like vias, tracks, pads, regions, fills, other polygons, etc. The connection style between the polygon and the same net object is defined in the design rules under the 'Plane > Polygon Connect Style' group. The rules will allow you to setup different connection styles (relief, direct, etc.) per polygon or object type if desired. For instance, I typically configure all vias as a direct connect style and all pads as relief connect style. If you have questions about configuring these rules, let me know. (FYI, just in case you reference Altium's current online help documents, the "air gap" option for thermals in Altium '13 or later is handled by the electrical clearance rule in Altium '10.)
The "Pour Over Same Net Polygons Only" will only connect the polygon to other polygons with the same net. No copper connections to the other objects will be made. As stated above, you'll probably want to stick with the "same net objects" option above.
Good luck.