For a MySQL query, how do you determine physical and logical I/O?
I recommend using Percona Server, for the slow query log enhancements.  I answered a similar thread to this on Stack Overflow:

https://stackoverflow.com/questions/3393206/what-is-the-equivalent-query-in-mysql/3443944#3443944

Take a look at this in particular (from http://www.percona.com/docs/wiki/percona-server:features:slow_extended?redirect=1#changes_to_the_log_format):

# User@Host: mailboxer[mailboxer] @  [192.168.10.165]
# Thread_id: 11167745  Schema: board
# QC_Hit: No  Full_scan: No  Full_join: No  Tmp_table: Yes  Disk_tmp_table: No
# Filesort: Yes  Disk_filesort: No  Merge_passes: 0
# Query_time: 0.000659  Lock_time: 0.000070  Rows_sent: 0  Rows_examined: 30  Rows_affected: 0  Rows_read: 30
#   InnoDB_IO_r_ops: 1  InnoDB_IO_r_bytes: 16384  InnoDB_IO_r_wait: 0.028487
#   InnoDB_rec_lock_wait: 0.000000  InnoDB_queue_wait: 0.000000
#   InnoDB_pages_distinct: 5
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