The entire web is just generated pixels on your screen.

Fits the ideal behind HTML HTML stands for "HyperText Markup Language"; its purpose is to mark up, or label, your content. The more accurately you mark it up, the better. New elements are being introduced in HTML5 to more accurately label common web page parts, such as headers and footers.

Although one thing you want to avoid is using frames in such a manner that the content of the site is in the frame and a menu is outside of the frame. Although this may seem convienient, all of your pages become unbookmarkable.

Iframes can have similar issues as frames and inconsiderate use of XMLHttpRequest: They break the one-document-per-URL paradigm, which is essential for the proper functioning of the web (think bookmarks, deep-links, search engines, ...).

The most striking such issue is probably that of deep linking: It's true that iframes suffer from this to a lesser extent than frames, but if you allow your users to navigate between different pages in the iframe, it will be a problem.