#1. The blog you've mentioned is very helpful and their book "High Performance MySQL" is worth purchasing. This is a very good book on databases in general and provides specific information about when to use the different backing engines that MySQL supports.

#2. As of version 5.1, nested subquery performance is exponentially slow. The following query will go exponentially slower as the number of records increases in TableA.

SELECT A.ID
FROM TableA A
WHERE
A.ID IN (
SELECT B.FK_ID
FROM TableB B
WHERE B.OTHER_COLUMN = '[Some Value]'
)

Reference link regarding performance: http://www.selikoff.net/blog/2008/12/10/memo-avoid-nested-queries-in-mysql-at-all-costs/

Note, this is being addressed in 5.4 (see: http://dev.mysql.com/tech-resources/articles/mysql-54.html Subquery Optimizations).

Yes, the query could be rewritten as an inner join (note EXISTS does not improve performance for this on MySQL). But reality is that there is a lot of SQL written this way. SQL that works just fine with SQL Server and Oracle. So caveat emptor.

#3. The slow query log is invaluable for finding said lousy queries (see: http://dev.mysql.com/doc/refman/5.1/en/slow-query-log.html). What's even nicer is that as of 5.1 it can be turned on and off at runtime (i.e. no server restart required).