How to remove 1000-row limit in MySQL Workbench queries?

You need to add your own LIMIT clause to then end of your query.

Use a number greater than the possible number of items that will be returned, say LIMIT 100000.

Source: http://wb.mysql.com/?p=230#comment-1279

Update:

(Using version 5.2.29CE, not sure how up to date I am):

On the menu bar visit Edit -> Preferences.

Jump to the SQL Queries tab.

In the Query Results section at the bottom untick the Limit Rows option.
You can adjust the limit to a higher value from this location as well, if that is preferable.

Update:

(Using version 6.3.4.0.828)

On the menu bar visit Edit -> Preferences. Expand SQL Editor. Select SQL Execution.

In the SELECT Query Results section, you can either uncheck Limit Rows or increase/decrease the Limit Rows Count.

Version 6.0 on Mac

Menubar->Query->Limit Rows->Don't Limit