Hi,
For gateway protocols:
SIP - newest, requires more understanding, quite a bit of configuration
H323 - most mature, most support, have to implement entire dial plan on gateway
MGCP - very easy, CUCM controlled gateway, only 3-4 lines of configuration on gateway, pretty good.
In general - if you let the correct ports through, any of them should be fine.
Use the commands:
show ip nbar port | i h323
show ip nbar port | i sip
show ip nbar port | i mgcp
These will tell you the ports you need on your firewall.
hth,
nick