How can I verify from the command line that all of the tables in my DB are InnoDB?

Count tables from each storage engine

SELECT COUNT(1) table_count,engine 
FROM information_schema.tables 
WHERE table_schema NOT IN ('information_schema','mysql') 
GROUP BY engine;

or to check each database's storage engine count

SELECT COUNT(1) table_count,table_schema,engine 
FROM information_schema.tables 
WHERE table_schema NOT IN ('information_schema','mysql') 
GROUP BY table_schema,engine;

or get a count all non-InnoDB tables ( should be 0 )

SELECT COUNT(1) table_count 
FROM information_schema.tables 
WHERE table_schema NOT IN ('information_schema','mysql') 
AND engine <> 'InnoDB';

To List Tables Names That are Not InnoDB and What Database the Table in Stored

SELECT table_schema,table_name 
FROM information_schema.tables 
WHERE table_schema NOT IN ('information_schema','mysql') 
AND engine <> 'InnoDB';

mysql> USE xyz;
mysql> SHOW TABLE STATUS;

It gives you the list of all tables and their engines.