It is interesting that you can pass the CCIE R/S lab exam with very little debugging, and a relatively short list of show commands - here are some of our favorites:

Catalyst

show vlan brief
show interface trunk
show interface switchport
show vtp status
show spanning-tree vlan

Frame

show frame map
show frame pvc

OSPF

show ip route ospf
show ip ospf database
show ip ospf neighbor
show ip ospf
show ip ospf interface
show ip ospf interface brief

EIGRP

show ip eigrp neighbor
show ip eigrp topology
show ip route eigrp
show ip protocol

RIP version 2

show ip route rip
clear ip route *
debug ip rip

BGP

show ip bgp summary
show ip bgp
show ip bgp neighbor x.x.x.x advertised-routes
show ip bgp regex
show ip bgp rib-failure
show ip route bgp

IP Multicast

show ip pim neighbor
debug ip mpacket
debug ip pim
show ip pim neighbor
show ip pim interface
show ip pim rp map
show ip mroute count
show ip mroute
show ip route

QoS

show policy-map interface