There are several guides for this online, but none seem to actually apply to release version 2.0.
To setup pfsense as a transparent firewall / bridge with 2 interfaces, follow these steps from a fresh install:
1. Disable NAT (but not the firewall). See http://doc.pfsense.org/index.php/How_can_I_completely_disable_NAT%3F#Disable_NAT
2. VERY IMPORTANT: As mentioned at http://forum.pfsense.org/index.php?topic=30653.0, go to the ‘System -> Advanced -> System Tunables’ and set net.link.bridge.pfil_bridge from ‘default’ to ‘1’
3. Bridge WAN and LAN by going to ‘Interfaces → Assign → Bridges’
4. Create OPT iface and assign the bridge to it by ‘Interfaces → Assign → Network Port’
5. Add an IP address to the bridge interface; this IP is the one you will use to access the firewall long term
6. Add allow all rules to ALL firewall interfaces to avoid being locked out. Ifaces OPT, WAN, and LAN
7. Set WAN and LAN interface type to ‘none’. (Under ‘Interfaces’ in GUI)
8. Disable DHCP server
9. The firewall should now be able to be accessed from all ifaces via the IP on the bridge from step 5
10. Carefully modify your firewall rules to be more restrictive. DNS, DHCP, etc.