You have 2 choices:
1) Ignore the phones based on CDP. You get this be just configuring 802.1X along with a VVID. Here's an example port config from a 3750:
interface GigabitEthernet1/0/2
description endpoints
switchport access vlan 2
switchport mode access
switchport voice vlan 200
srr-queue bandwidth share 10 10 60 20
srr-queue bandwidth shape 10 0 0 0
queue-set 2
mls qos trust device cisco-phone
mls qos trust cos
dot1x pae authenticator
dot1x port-control auto
spanning-tree portfast
spanning-tree bpduguard enable
ip verify source
ip dhcp snooping limit rate 10
The config above will allow a Cisco phone in "for free" just b/c it can do CDP.
2) Authenticate IP phones via 1X or MAC-Authentication for phones that cannot support 1X. This would be the same config as above, with the addition of this line:
dot1x host-mode multi-domain
And if your IP phone cannot do 1X (for example the 7940 cannot) then you'll need to check it's MAC for entry into the network by adding this line:
dot1x mac-auth-bypass
Hope this helps,