When I receive an e-mail invitation via Google Apps, there are two places where it asks if I'm going, and I'm never sure which one to click (see screenshot). Does it matter which one I click? What's the difference, and why does it always ask twice?
There is no difference. The reason there are 2 is because top response is a Gmail add-on that recognizes a Google Calendar invitation, and then displays a Calendar widget to make it easier for you to reply.
The second is the actual invitation email message, which does include RSVP links in the body text. The reason you see both is just that Gmail will add the widget automatically. If you invite a non-Gmail user, they will only see the email body text, and will have to use those links.
My personal preference is to use the top links for 2 reasons: