Is there a way to add or remove programs to/from my Ninite installer?

You can't modify your current installer, but for the next time:

• Check the apps you want
• Click the Get Your Ninite button
• On the next page (where the download begins), you get a link named change apps
• Save this link to your bookmarks

This link brings you to the ninite page with all you apps pre-checked, so you can easily add/remove some apps as needed.

You couldn't do this with the free website based ninite software download- its a feature of ninite one which is part of the paid ninite pro service, as opposed to a standalone product.