Prasanth,
Yes MQSeries adapter comes out-of-the box with biztalk server 2006. You might be looking for it when you are desigining the orchestration and binding the Receive port at design time, there we can see only four adapters which doesn't contain MQSeries (I dont know why is this). Leave your binding to Specify Later and after deploying the project make a new Receive port in the Biztalk Administration Console, there you'll be able to see all the adapters that come with Biztalk server 2006, including MQSeries. If you still cant find it there, Go into the Platform Settings (Within Biztalk Administration Console) –> Adapters, right click and add a new adapter for MQSeries.
I've tried to use it with MQSeries queues running on Windows and it works fine, but I am not too sure about Unix AIX.
Hope this helps
Regards,
Sajid.