As far as I know there isn't an 'all' switch for the ec2-terminate-instances command. So you probably need to script it. It won't be that hard. You only need to generate a comma separated list of your instances.
This is a python script I am using:
from boto.ec2.connection import EC2Connection
conn = EC2Connection('', '')
instances = conn.get_all_instances()
for reserv in instances:
for inst in reserv.instances:
if inst.state == u'running':
print "Terminating instance %s" % inst
if __name__ == "__main__":
It uses boto library. This is not necessary for the specific task (a simple shell script will be enough), but it may be handy in many occasions.
Finally are you aware of Elasticfox extension for Firefox? This is by far the easiest way to access EC2.