As advertisements become ever more annoying on the web, people are developing ways to fight back against the intrusion. Exactly how they do so brings up some subtle issues in how ethical that is, because there are several types of techniques with different ethical implications.
Browser-based blocking
Browser-based blocking is probably the easiest blocking technique there is, and if you didn't know about this before, consider this your reward for slogging through the essay this far. In the latest versions of Mozilla and derivatives, there are simple options to prevent pop-up windows for appearing. For instance, in Mozilla 1.3, going to Edit->Preferences, opening the Privacy and Security tab, and clicking on the Popup Windows text, will show a dialog that allows you to turn off pop-up windows. It's really nice in 1.3 and above because you can enter exceptions, if you have certain sites which require pop-ups to work correctly but you trust them to use pop-ups in a manner you approve of. In addition, in the Images section (just above "Popup Windows"), you can tell images not to animate, which for the most part only affects advertisements. And finally, if you open the Advanced list and click on Scripts & Plugins you can disable a whole raft of "features" used mostly to annoy the user.
I personally recommend using Mozilla and activating these features, and leaving Internet Explorer only for things that absolute require it. Generally, after taking these steps the annoyance at the advertisements subsides enough that you don't feel the need to do the more extreme things I'm about to discuss.
Two interesting things about this: First, not all browsers even support the idea of opening new windows in the first place, so it can't be that big a deal to tell your browser not to open new windows. Second, everything I mentioned is solely under the users control, and none of these things depend on the content of the web page. All animating images will not animate, without regard to whether it's an advertisement or who created it. No pop-up windows open, unless they are from an approved site, without regard for what they will contain. These features are independent of the content. They happen to mostly affect advertisements but that's a consequence of the fact that mostly advertisers (ab)use these features. None of these settings do anything to block the simple, pure-text ads that Google.com uses, for instance, showing they are not directly targeting advertising.
Based on that analysis, there's certainly nothing wrong with configuring your browser like this, because as we've mentioned earlier, web pages are not unbreakable contracts to display certain things in certain ways, they are loose instructions for assembling images on the screen to the browser, and the browser and the browser user are free within the parameters of those instructions to render the content in many ways.
Some people are developing technologies that try to detect when the user is blocking popups and not allow them to proceed without viewing the ads. It is probably not ethical then to bypass these checks, as the content owner is clearly making access contingent on the ad viewing, which is within their rights. It's probably not a good idea to annoy a consumer that devoted to dodging ads, though, and it's unlikely the contents of the ad will leave such people with a favorable impression, so hopefully the open market will realize this and an arms race will not be necessary.
Filtering Proxies
The most sophisticated ad-blocking solutions are filtering proxies. The proxy works as in the proxy-based annotator, but instead of adding information, it takes it away.
An example of such a program is The Internet JunkBuster Proxy(TM), which can block certain URLs (including that of advertising images), and prevents certain information from being transmitted to web servers that most browsers send by default, such as cookie information. As seen in the annotation example, a proxy server can transform content in nearly any imaginable fashion, so the mature ones such as The Internet JunkBuster Proxy(TM) are very flexible and powerful.
Used as a tool by a single user, again I don't see any significant problem with such software, again because the "contract" of the web is not that the user must see all content precisely as intended by the author. A single user adding sites to his filtering proxy is similar to simply refusing to visit those sites, which it is in the power of the receiver to do. Some browsers, such as the variants on Mozilla, even build this into the browser; by right-clicking on an image you can tell the browser to stop loading images from that server.
There is an obvious scaling problem with this, though, in that advertising sites are popping up faster then a user can smack them down, and there is obviously a lot of redundancy in what each user does, as many of them choose to block the same sites. It seems like it would be a good idea to create a tool with a centralized list of bad sites, let users update it dynamically, and distribute software that checks the centralized database for what should be blocked. One piece of software that does this is Guidescope.
Unfortunately, this crosses the same line that annotation software does, by allowing third parties to influence the communication without the permission of the sender. It seems like it would be nice if we could salvage the ability to use this ethically, but that's an artifact of considering only the receiver's point of view. In the larger context, this must be considered a form of censorship and the limited benefits to certain people do not justify how dangerous it is to open the doors to censorship... even if you are yourself one who would benefit. Acting ethically is not always pleasant in the short term.
Using a filtering proxy as a tool is acceptable, until the proxy is using input that did not come directly from the user. This also implies that while it's OK to distribute the proxy server, the list that it uses to block sites with should start out empty so that only the user's input is used by the program.
Practically speaking, I find that using Mozilla and blocking popups and animating images, and optionally telling Mozilla to be conservative about what cookies it accepts, takes care of the majority of the problem with privacy and annoying advertisements without the use of unethical group censorship programs, so once again the benefits of such a scheme are quite marginal compared with the real damage to free speech (even commercial free speech) such programs do.