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A stack is the set of programs that are combined to create a software system. The most common example of a stack is LAMP (Linux, Apache, MySQL, and PHP/Perl/Python). On Ohloh, a stack is a collection of all the open source projects you use.
What goes into your stack is completely up to you. Add any open source projects you use: tools, libraries, frameworks, etc.
There are three ways:
From the main page of a project, e.g. Subversion, click on I USE THIS in the Users area:
You'll now be able to pick the stack to add the project to, or can pick to create a new stack with this project.
From your stacks page, you can navigate to one of your stacks. The Recommendations panel will pick projects you're likely to find interesting. Click I USE IT on any suggestion you like:

Your stacks page has a New Stack button on the top right. Click it and you have a new stack. Change the stack name and description by clicking on them and typing.
Consider creating a different stack for each software system you develop, maintain, use. For instance, your database server likely runs a stack that is quite different from your development machine which might be quite different from your webserver. Some other stacks: Home, Gaming. Add whatever you want.
Ohloh now counts the number of people who use a project, rather than number of stacks. Including a project in multiple stacks will not increase it's User count.
Ask your users to come to Ohloh, register for an account and stack your project. This increases your User count and makes your project more appealing to potential users.
Ohloh has stack widgets that you can embed. Click Embed on the stacks or an individual stack page to get started. Here's a sample:

It might be because the page is being rendered by IE6 in quirks mode. If you have control of the page, you can fix this by adding a xhtml preamble, e.g.:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">