Sharepoint development: application or custom pages?

I was reading my hero and just wanted to put a note regarding application and custom aspx page.
Application pages are placed in layout folder in hive and mapped to virtual folder /~layouts. They do not use the master pages of the site at all, they have their own master pages.
Custom pages are site-specific.

If you were thinking which type of pages you should use, I just wanted quoted from the my hero's book:
"This {/~layouts} virtual directory is shared between all sites in the entire farm...If you want your page to be accessible only to a certain site or site collection, it makes sense to package the pages as a module and make that module part of a feature. That way, you can deploy or retract the page or pages on a site-site basis."

SharePoint 2010:
"One noteworthy improvement to the SharePoint 2010 user interface is that application pages can now link to master pages in the master page gallery.  "
Understanding Visual Upgrade in SharePoint 2010