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They can generally be used like line card ports. On some 4500 sups, with dual sups installed, there can be special usage considerations whether all sup ports are available for usage. On some 6500 sups, there can be QoS differences, based on configuration, whether all sup ports are enabled.
Normally, these ports might be used for uplinks (e.g. link from edge role chassis to distribution device) for the whole chassis because sometimes (especially with older line cards), sup ports have more bandwidth and/or support fiber.
6500s and/or 4500s often use at least some of their sup ports to support VSS.
