Port aggregation (in the cisco world known as channelling) combines two ports for increased bandwidth and link redundancy for connecting switches together.

Router# configure terminal
Router (config)# interface range Gi0/45-46
Router (config-if)# channel-group 1 mode desirable
Router (config-if)# ^Z

This will link ports 45 and 46 (example is on a 2960 switch) together and assign them to group 1. By setting the link mode to desirable, the ports negotiate the proper PAgP protocol. This example configures a group a of ports at the same time. You can always configure each port individually by using the standard "interface Gi0/45" command. Once ports are assigned to a channel group, you can add configuration options to all ports by adding them to the channel. To configure the channel, use the following command: "interface port-channel 1". The channel group number is unique on the switch. Both switches need to be configured the same, though the channel number does not need to match. When choosing which ports to use for channeling, be sure to choose ports not sharing switch bandwidth to ensure maximum throughput. Ensure that spanning-tree is on in order to prevent loops.