Alcatel Unleashed

What would be the best way to connect a 2008 server to 2 x 6400 switches that are stacked at the back with 10gb cables ,we have no budget restrictions.

I don't understand this question. What is the purpose of your question (wich port? ...)

In my opinion if the 2x 6400 are stacked you can connect with two NIC's in 2008 server one to one switch in stack and second to another switch in stack i don't know if 2008 server can make something like link aggregation (i use linux/unix servers) if yes you can make something like link aggregation between server and stack.

Well, the best should be a 4 x 10G Gbics in both switches and two 10GB fibre cards in server, i think, if you don't have budget savings.
Lot cheaper and more appropriate would be to go with Copper 1 GbE but have two servers in HA (each server with two links to different switch) .

os6400 use 10gb only in stack you can't connect switch to servere via 10g uplink only aggregation on rj45 ports, something like multi chassis link aggregation

Ok, you are right, only from 6850+ you could use a SFP-10G-SR* family
So, only a copper 1Gbe link aggregation, like 4 times with good NIC on server side.

Most servers do support IEEE802.3AD link aggregation. So if you have multiple NIC's in your server best would be to have at least one connecting to switch stack number 1 and the other nic to the second switch stack member. This will give you effectively a 2 gigabit connection, loadbalancing and failover. You can also expand to a maximum of 8 connected nic interfaces on the server.