In a multi-VLAN port, the port will pass the specified VLANs over it while a trunk passes all the VLANs by default. If you are connecting 2 switches, trunk is the way to go. If you want to you can clear of the uneccessary VLANs.
The only scenario I can think of Mutli-VLAN feature being useful is if you have a server and if you want clients from multiple VLANs to access it, you can make the server port a multivlan port.
Note
1)Only XL switches support Multi-VLAN port feature
2)Multi-VLAN and trunks cannot co-exist