Table corruption: How to perform Innodb Checksum checks in MySQL 5.5 for Windows?
ANSWER #1
This feels clumsy doing this in Windows but here it goes. If you are able to login to mysql, then run this script
set MYSQL_USER=root
set MYSQL_PASS=rootpassword
set SQLSTMT=SELECT CONCAT('REPAIR TABLE ',table_schema,'.',table_name,';')
set SQLSTMT=%SQLSTMT% FROM information_schema.tables WHERE engine='InnoDB'
set MYSQL_CONN=-u%MYSQL_USER% -p%MYSQL_PASS%
echo %SQLSTMT%
mysql %MYSQL_CONN% -ANe&quot;%SQLSTMT%&quot; &gt; C:\windows\InnoDBCheck.sql

After you run this script, add this to my.ini
[mysqld]
init-file=C:\windows\InnoDBCheck.sql

Then, restart mysql
net stop mysql
met start mysql

during the startup, just after crash recovery, the
Forgive me for such a crude solution since I have very little dealing with MySQL for Windows (that's not sarcasm, I am serious).
ANSWER #2
Here is something more serious
I just checked my MySQL 5.6.10 no-install ZIP file. It has innochecksum.
C:\&gt;dir \MySQL_5.6.10\bin\i*
 Volume in drive C has no label.
 Volume Serial Number is 2C92-485B

 Directory of C:\MySQL_5.6.10\bin

01/22/2013  07:05 PM         4,065,792 innochecksum.exe
01/22/2013  07:05 PM         3,706,880 innochecksum.pdb
               2 File(s)      7,772,672 bytes
               0 Dir(s)  160,596,770,816 bytes free

C:\&gt;

Download that ZIP and try running that .
You could then collect all the .ibd files with something like this:
cd &quot;C:\Program Files\MySQL\MySQL 5.5\data&quot;
dir *.ibd /s/b &gt; C:\ibdfiles.bat

You can then edit C:\ibdfiles.bat and prepend innochecksum against every filename.
Sorry this is not a full answer, but at least you can a hold of innochecksum.exe