InnoDB and MyISAM each have their strengths and weaknesses.

• May 03, 2012 : Which is faster, InnoDB or MyISAM?
• Sep 20, 2011 : Best of MyISAM and InnoDB

If you have enough RAM, I would choose InnoDB because it caches data and index pages in the Buffer Pool. MyISAM only caches index pages in the Key Cache.

MyISAM tables experience full table locks for each INSERT, UPDATE, and DELETE. MyISAM tables always require disk access for data.

InnoDB tables always incur disk I/O in the following areas:

• Double Write Buffer : Changes are posted in ibdata1 to avoid OS caching
• Insert Buffer : Changes to Secondary (non-Unique) Indexes as posted in ibdata1
• Data and Indexes
  • With innodb_file_per_table = 0, changes are written to ibdata1
  • With innodb_file_per_table = 1, changes are written to .ibd tablespace file. Read I/O against ibdata1 still necessary to crosscheck table metadata

SUMMARY

In an environment with the following:

• heavy writes
• heavy reads
• tons of RAM
• heavy connections

I would always choose InnoDB. Please check out my other post about InnoDB over MyISAM : When to switch from MyISAM to InnoDB?

When would I every choose MyISAM?

Under the following scenario

• Using MySQL Replication
• Master with all InnoDB
• Slave with all tables converted to MyISAM
• ALTER TABLE ... ROW_FORMAT=Fixed for all tables on the Slave

Disk I/O wise, MyISAM has a slight edge with ROW_FORMAT-Fixed because you only interact with one file, the .MYD file. The row size is completely predictable because VARCHAR is treated as CHAR this shortening access time for data retrieval.

• May 10, 2011 : What is the performance impact of using CHAR vs VARCHAR on a fixed-size field?
• Mar 25, 2011 : Performance implications of MySQL VARCHAR sizes

On the other hand, InnoDB has to interact with multiple files (ibdata1, serveral read/write threads upon the .ibd of the InnoDB table).

You cannot have multiple columns being returned in a subquery like that, so you have several ways that you would have rewrite this query to work.

Either you can unpivot the data in the team table so you are only returning one column:

select * 
from players 
where sport='football' 
  and position='DEF' 
  and pname!='Binoy Dalal' 
  and pname not in (select player1 
                    from team where sap='60003100009'
                    union all
                    select player2
                    from team where sap='60003100009'
                    union all
                    select player3
                    from team where sap='60003100009'
                    union all
                    select player4
                    from team where sap='60003100009'
                    union all
                    select player5
                    from team where sap='60003100009'
                    union all
                    select player6
                    from team where sap='60003100009'
                    union all
                    select player7
                    from team where sap='60003100009'
                    union all
                    select player8
                    from team where sap='60003100009') 
order by price desc;

Or you can use a NOT EXISTS query:

select * 
from players p
where sport='football' 
  and position='DEF' 
  and pname!='Binoy Dalal' 
  and not exists (select *
                  from team t
                  where sap='60003100009' 
                    AND
                    (
                      p.pname = t.player1 OR
                      p.pname = t.player2 OR
                      p.pname = t.player3 OR
                      p.pname = t.player4 OR
                      p.pname = t.player5 OR
                      p.pname = t.player6 OR
                      p.pname = t.player7 OR
                      p.pname = t.player8
                    ))
order by price desc;

Or you would have to use multiple WHERE filters on the player name:

select * 
from players 
where sport='football' 
  and position='DEF' 
  and pname!='Binoy Dalal' 
  and pname not in (select player1 
                    from team where sap='60003100009')
  and pname not in (select player2 
                    from team where sap='60003100009')
  and pname not in (select player3 
                    from team where sap='60003100009')
  and pname not in (select player4 
                    from team where sap='60003100009')
  and pname not in (select player5 
                    from team where sap='60003100009')
  and pname not in (select player6 
                    from team where sap='60003100009')
  and pname not in (select player7 
                    from team where sap='60003100009')
  and pname not in (select player8 
                    from team where sap='60003100009')
order by price desc;

However, ideally you should consider normalizing the team table so you have one column with the player name and another column that assigns them a player number. Similar to this:

create table team
(
  player varchar(50),
  playerNumber int
);

Then when you are searching the team data you only have to join on one column instead of 8 different columns.