I'm trying to setup trunking on a netapp connected to a Cisco 3550 gigabit switch (OS vers.12 on the switch).

Sorry no experience with this switch...

The odd thing is that when I setup two gigabit lines trunked together from the netapp to the switch I saw no improvement in thoughtput compared to a single gigabit line.

Again, not familiar with this particular switch...however, I have setup an enviornment similar to what you described and did see performance increase instantly.

Extreme Summit 200-48 with a FAS250. I created a single vif interface out of the 2 gige interfaces on the FAS250 and enabled sharing on the switch ports that they plug into. I then took two 10/100 cards on a server and bound them togther and enabled sharing on the ports for the switch too. I went from pushing about 10MB/sec from the server to 20MB/sec. As this is well below the theoretical maximum for two gige ports trunked together, 250MB/sec (125MB/sec each), the problem is that pushing so little data makes it hard to see how effectively the gige trunk works.

So, to answer your original question, yes I have done it; but utilizing 10/100 cards doesn't do justice when testing performance on a gige device.