How do route traffic from internal SAN subnet through Cisco Catalyst 6509?

Each subnet is on a separate VLAN, you should configure all VLANs on the 6500 switch. Then, for every vlan that you need to have routing, use as a gateway the ip address of the VLAN on the catalyst.

Add a default route at the 6500 pointing to your firewall for unknown routes. The 6500 should handle all the inter-VLAN traffic routing.

You dont have to use trunk ports on the other switches that are connected to the 6500 if their equipment only belongs to one VLAN.

I understand how to do what you've suggested, but is there a way on the Catalyst 6500 to designate one port as a routing port, connect that to my Internet facing router, or to my firewall, and route traffic from the SAN subnet to the Internet?

The SAN subnet is just another VLAN. Whats the purpose of doing that?
If you do not want to have a default route to the router of firewall you can add a static route for the destination subnet, or even a policy route, if you want traffic from the SAN subnet to be treated differently.
All ports are capable of being routed.
If you want to have a router only for routing the SAN subnet traffic, you can connect it in an access port, on the 6506, any VLAN (it does not have to be the same as the SAN subnet), and route the SAN subnet traffic with policy routing through that router, and use your default route for the others.

Can you provide the commands or point me to a link that will help me set that up on the Catalyst 6509?

Which scenario? Policy routing the SAN VLAN traffic through one router connected at another port ?
You only need policy routing if you want the SAN VLAN traffic to use another gateway than your normal gateway. If you want to read more:
http://www.cisco.com/en/US/docs/ios/12_2/qos/configuration/guide/qcfpbr_ps1835_TSD_Products_Configuration_Guide_Chapter.html

ip routing
int vlan 1
ip address 192.168.1.1 255.255.255.0
!
int vlan 2
ip address 192.168.2.1 255.255.255.0

ZuluGr,

Okay, I think I've got it now.  The Catalyst 6509 is connected to a subnet (10.10.10.x) that has access to a gateway (10.10.10.251), with no routing statements on the Catalyst (using a cross-over at the moment).  If I plug a cable from each SAN Switch (10.10.6.x) into the 6509's switchports, or do I have to make the ports I plug them into routing ports?, then I should be able to use policy routing to tell the 6509 that packets from those source addresses are going to route out to 10.10.10.251.  Is this correct?

If 10.10.10.251 is your 6506's default gateway, and you have routing enabled on the switch (ip routing), then the 10.10.6.x subnet will automatically be routed to your default gateway for internet access. For example the 10.10.6.x subnet is VLAN 10 and the ip of VLAN 10 on the 6506 switch is 10.10.6.1, then if the devices on the 10.10.6.x subnet use 10.10.6.1 for their gateway, the will be routed to  the 10.10.10.251. ( assuming you have set the command 'ip route 0.0.0.0 0.0.0.0 10.10.10.251' on the 6506 switch, and 10.10.10.251 is the ip address of your wan router/firewall that is connected to the 6506 at another VLAN.

I know all of this because I've done exactly what you've mentioned before :) but the 10.10.6.x subnet is completely separate and I don't want to put a global route statement or a VLAN relating to them on the 6509 right now. Devices on the 10.10.6.x are not going to use the 6509 as their global gateway...they just need to get to the Internet for calling-home issues that they may have.  

If you do not want to put those on the 6509 as a VLAN and just need them to have internet access, you can directly link them with your router/fw.
If you dont want to create a VLAN  for those in the 6509, why not connecting the 2960 to the firewall? Put a secondary IP (10.10.6.x) at the firewalls internal interface, and use that as their gw