Drupal 7 Uses InnoDB, so do I need other configs? If I'm optimizing a database that will be delivering multiple Drupal 7 websites, all using InnoDB, do I need to worry about [myisamchk] &amp; [isamchk] sections, or can I just worry about the stuff within [mysqld]?

I'm assuming if I delete these sections, that the defaults will just kick in if they are needed.  

I'm trying to document, outline my.conf best practices here http://groups.drupal.org/node/289613
The other group headers have no bearing on InnoDB whatsoever. [mysqld] is all you really need.
With regard to InnoDB itself, you will need to tune InnoDB in many aspects
System Tablespace / Individual Tablespaces

Sep 26, 2012 : How do I shrink the innodb file ibdata1 without dumping all databases?
Jul 05, 2012 : Move ibdata1, set innodb_data_file_path
Apr 19, 2012 : MySql - Clean ibdata1
Apr 01, 2012 : Is innodb_file_per_table advisable?

Buffer Pool

Oct 22, 2012 : How much memory do I need for innodb buffer pool?
Jun 13, 2012 : What to set innodb_buffer_pool and why..?

Transaction Logs

Jan 17, 2013 : MySQL 5.5 - Innodb - innodb_log_file_size higher than 4GB combined?
Feb 16, 2011 : How to safely change MySQL innodb variable &#39;innodb_log_file_size&#39;?

Multiple CPU / Multiple Core Engagament

May 21, 2012 : MySQL - Installing InnoDB Plugin
Mar 16, 2012 : Using multiple cores for single MySQL queries on Debian
Nov 24, 2011 : Why mysql 5.5 slower than 5.1 (linux,using mysqlslap)
Sep 20, 2011 : Multi cores and MySQL Performance
Sep 12, 2011 : Possible to make MySQL use more than one core?

Epilogue
There are so many other aspects I have no time to write about because I probably have written it already. Please see all my posts on InnoDB.
What is also worth noting is that you should be using the latest version of MySQL

MySQL 5.6.10 now supports FULLTEXT indexing. You need to test this fully.
InnoDB in MySQL 5.6 is faster than InnoDB in MySQL 5.5

On a side note, did you know the StackExchange has a Drupal Q&amp;A site ? I have posted answers there as well.