As I understand it, this message is not a bug, it's a "feature."
Users often open a lot of windows and tabs in Safari. Each tab may contain numerous scripts, some of which continue running all the time, unbenownst to you (e.g., refreshing data from the parent site). Pages with complex content can also consume a lot of memory, and this memory is not always freed when you close the page. As a result, after a long session with a lot of browser windows open, Safari can become very bogged down -- short of memory (possibly swapping data from memory to disk and back), and working hard to keep every page's scripts running. Also, in older versions of Safari, if one page somehow crashes Safari, the whole web browser would close and you would lose your entire current session.
Before about version 5.1, Safari just kept chugging along in this degraded state. But around version 5.1, Apple took a new approach. They split the web browser into two applications - "Safari" and "Safari Web Content". "Safari" is the outer shell. It remembers which windows and tabs you have open, the size of each window and scroll position for each tab, and the current URL and browser history for each tab. "Safari Web Content" manages everything inside each tab -- it composes the text and graphics, runs the browser scripts and plug-ins, etc. Now, if one page manages to crash the browser, "Safari Web Content" just gets killed and reloaded, using the information remembered by "Safari." As currently configured, "Safari Web Content" reloads the frontmost tab of every window automatically, and then reloads additional tabs the first time you click on them.
So far so good. But Apple decided to go one step further, and whenever Safari notices that "Safari Web Content" is bogged down, it presents the "Some webpages are not responding" dialog box. What this dialog box is really offering is to force "Safari Web Content" to quit and restart, restoring your current state as described above.
I would really like this dialog box to include a third option, something like "Continue without reloading". This would maintain the pre-5.1 behavior -- load a new page without reloading all your windows, even if Safari Web Content is barely grinding along. (And often if press Cancel and then wait a few minutes for Safari to settle down, this is approximately what I get.) I'm pretty sure that adding this third option would take Apple about 30 seconds of code-writing, but they probably consider it too hard to explain to average users. Maybe they could enable a button like this via a secret preference setting instead?
I say this because restarting Safari Web Content (as this dialog box does) has several negative side-effects.
(1) If you are in the middle of filling in a form or accessing a web server that doesn't have good session persistence, you will lose your current work. Sometimes you'd rather load a new page slowly than give up all your active sessions.
(2) Restarting Safari Web Content causes a blast of Internet activity as Safari reloads the frontmost tab of every window. This takes a while to settle down. Sometimes you just want to access one more page without waiting for all these pages to reload.
(3) This is a bug that may be easy to fix, but for now it counts as another drawback: whenever Safari Web Content restarts, all tabs except the frontmost tab in each window become invisible for the purposes of "Add bookmarks for these tabs..." or "Reopen all windows from last session...". So after restarting Safari Web Content, if you bookmark the tabs in a window, or close Safari, and then try to restore your tabs later, you will get a nasty surprise - only the frontmost tab will be remembered. This can be mitigated by manually activating every tab in the window before bookmarking the window or quitting Safari, but that's just a workaround for a fairly amateur bug.
(4) Just to gripe a bit more, point (1) causes particular problems with my university library's proxy server. Whenever I try to access subscription content, the proxy server redirects me to a login page, then back to the publisher's page, where I am treated as a paid subscriber. Once logged in, the proxy server will let me access other protected pages from any publisher for a few hours without needing to login again. Later, after my proxy server session has expired, if I reload a protected page, the proxy server shows me a new login page, then redirects my browser back to the page, which is fine. But if I allow Safari Web Content to be reloaded after a proxy server session has expired, then Safari tries to reload every page simultaneously. In this case, every single page gets redirected to the login page, and then our (admittedly lame) proxy server redirects every single page to a single URL, the first page that was reloaded. After this, there is no way to get back to my original pages, and I lose all trace of numerous articles that I previously opened and intended to review for my research. This problem can be avoided by logging in to the proxy server using a different browser before clicking the "Force Reload" option in Safari. But if I forget to do that and just click "Force Reload", I can lose a lot of work.