Linux Transparent bridge

First you need to install the bridge-utils:

apt-get install bridge-utils

Configuring the bridge:

ifconfig eth0 0.0.0.0 promisc up
ifconfig eth1 0.0.0.0 promisc up
brctl addbr br0
brctl addif br0 eth0
brctl addif br0 eth1
ifconfig br0 1.2.3.4 netmask 255.255.255.0 up
route add default gw 1.2.3.4 dev br0

In this example, I suppose you are using eth0 and eth1. In the ifconfig line, I assigned IP address 1.2.3.4 to the bridge so I can access it remotely. Use an IP address in your network.
You may check that the bridge is working by using tcpdump:

# tcpdump -n -i eth0
...
(lots of funny stuff)
...
# tcpdump -n -i eth1
...
(lots of funny stuff)
...

Plug your machine into the network, and everything should work. Your Linux box is now a big, expensive two-port switch.

Making the Bridge Permanent

Edit the file /etc/network/interfaces and add:

auto br0
iface br0 inet dhcp
bridge_ports eth1 eth2
bridge_stp on