You should use a Layer 2 etherchannel if your Switching Topology is Layer 2 i.e. you rely on Spanning Tree Protocol to manage the redundancy etc. If in case you are running any routing Protocol in you LAN and essentially your LAN topology is L3 you can go ahead and configure a layer 3 etherchannel.
Theres one major difference between L2 and L3 etherchannel which dictates the traffic flow and thats Load Sharing/Balancing across the individual links.
A L2 ether channel can load balance using Source Mac, Destination MAC or a combination of both only whereas a L3 etherchannel can Load balance using Source IP, Destination IP, or a combination of both and on Cat 4500/6500 a Layer3 Etherchannel can Loadbalance using Source Port, Destination port or a combination of both.
So i hope you can decide which one to use but be consistent with your LAN topology (L2 or L3)
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