We have a custom workflow in a SharePoint 2007 web-application and would like to use the same workflow in another web-application (SharePoint 2007).
How can we achieve this? do we have any migration tool?
If this is an SPD Workflow, you can try MetaVis Migrator. It will move workflows between site colelctions.
The easiest approach is to package your source code binaries to WSP. You can use WSP builder for SharePoint 2007 and deploy to any site web-application you need.
If the workflow was created via SharePoint Designer, I don't know of any way to "migrate" or reuse it without either breaking it in some way, or paying for a 3rd-party tool. I've tried free tools that help fix the GUIDs, but they don't seem to fix the workflows reliably. I've ended up having to recreate those workflows from scratch.
The best thing to do is package it as a wsp as Toni says above. Another great tool is Nintex - it's all WYSIWYG in-browser, and you can save workflows as templates & re-use them anywhere (though it's not cheap).