<p>I would like to make the update of the web application as automated as possible.<br>
I'm looking for a tool that can compare two instances of a database and generate an update script for me. As part of the build process create a instance of the last version of the database (ie currently in production) and compare that to what has been changed on the development version.  </p>

<p>Any input is appreciated.</p>

See
Mechanisms for tracking DB schema changes
I believe the
profluence
of this question on SO speaks to the lack of a standard solution to this problem.
The great divide in approach is
- write delta scripts
- automate script generation from a "master" instance
It sounds like you want something in the latter camp.
Several such solutions and tools are noted in the above question.