In VS 2008 (and previous versions), when you opened the “Tools”, “Customize…” dialog, “Commands” tab, you got a list of  “categories”, and each category has a list of commands that you could drag and drop on some toolbar to create a button from that command. For commands provided by add-ins, you had the “Add-Ins” category and for commands provided by macros you had the “Macros” category. Furthermore, you had a “Rearrange Commands…” button where a new dialog allowed you to select a menu bar or a toolbar, and add/move/remove commands (buttons), etc. So far so good, except one thing that VS has never managed well which is that toolbars, menu bars, commandbar popups and buttons provided by add-ins can be temporary if the add-in uses that approach instead of the permanent one, and therefore Visual Studio should not offer the temporary UI items of add-ins for customization, since customization will be lost when the add-in is unloaded and when loaded again the add-in will recreate the UI from scratch. I discussed these issues in detail in the article:

HOWTO: Handling buttons and toolbars user customizations from a Visual Studio add-in
http://www.mztools.com/articles/2008/MZ2008019.aspx

In VS 2010 (Beta 2), commandbars are WPF-based and the Customize dialog has suffered a re-design, but if it is not fixed in the RC / RTM builds things are getting worse due to these bugs (currently under evaluation, but likely closed as “won’t fix” in this release):

VS 2010 Beta 2 Bug: wrong customization for commandbarpopup of add-ins
https://connect.microsoft.com/VisualStudio/feedback/ViewFeedback.aspx?FeedbackID=501255

VS 2010 Beta2: Add-ins and macros commands should not appear in the
“Tools”, “Customize” dialog, “Commands” tab, “Menu bar” combobox
https://connect.microsoft.com/VisualStudio/feedback/ViewFeedback.aspx?FeedbackID=512141

Those bugs will cause confusion to users of add-ins if they try to use the Customize dialog…

At least these two minor bugs were fixed after Beta 2:

VS 2010 Beta 2 Bug: Command picture not shown in Tools, Customize window, Commands tab
https://connect.microsoft.com/VisualStudio/feedback/ViewFeedback.aspx?FeedbackID=502250

VS 2010 Beta 2 Bug: Command name shown instead of caption in Tools, Customize window, Commands tab
https://connect.microsoft.com/VisualStudio/feedback/ViewFeedback.aspx?FeedbackID=502242