A number of protocols utilised in the Link Layer are listed here
Spanning Tree Protocol
The Spanning-Tree Protocol (STP) is an algorithm employed by bridges and switches to try and ensure that switching loops do not occur in the network topology. Capable of shutting down redundant links until they are needed, STP is a staple for enterprise networks. There have been many different types of the spanning-tree protocol to appear over the years such as the Multiple Spanning-Tree Protocol (MSTP), Per-VLAN Spanning-Tree Protocol (PVST), Rapid Spanning-Tree Protocol (RSTP), and Rapid Per-VLAN Spanning-Tree Protocol (RPVST).
Spanning-Tree Protocol (IEEE 802.1D)
Multiple Spanning-Tree Protocol (IEEE 802.1Q-2003)
Per-VLAN Spanning-Tree Protocol (Cisco Proprietary)
Rapid Spanning-Tree Protocol (IEEE 802.1w)
Rapid Per-VLAN Spanning-Tree Protocol (Cisco Proprietary)
The Rapid Per-VLAN Spanning-Tree Protocol is a Cisco enhancement to the standard Per-VLAN spanning tree protocol that existed before it. One of the major advantages of this protocol is that it converges much faster than Per-VLAN STP and it also has a concept of "Alternate" backup ports in the event the elected root port goes down to that it doesn't invoke the STA (Spanning Tree Algorithm) which can utilize CPU cycles and cause network outages by bringing down links.
Cisco Discovery Protocol (CDP)
This is a Cisco proprietary protocol that is extremely useful in network documentation. When this is enabled on the switch and per interface one could log into a switch and issue a simple command to find all connected routers and switches and what ports they are connected to both locally and on the remote device. This also includes things like model and sometimes IOS version. Cisco recommends that this protocol ONLY be ran on devices where it needs to be run and on those devices to only enable CDP on the specific ports. If these are enabled on ports connected to a PC a user could utilize a traffic sniffer to pick up on the information transmitted.
Link Layer Discovery Protocol (IEEE 802.1AB)
Unlike the above CDP this is a vendor neutral "device discovery" protocol that operates at the link layer. On Juniper and HP switches you will utilize this instead of CDP (since CDP will not be available) to perform discovery devices connected to your switch.
VLAN Trunking Protocol - VTP (Cisco Proprietary)
The VLAN trunking protocol is a Cisco proprietary link layer protocol that propagates VLAN database information from a VTP switch designated as a VTP server to all other switches in the network ask to keep all VLAN databases in the network consistent.