Feld0's leviathan spiel on all things ads, ad blockers, and how they make and break the Internet.
Ahem. Don't take my position as a web developer and site operator as that of the opposition. Those who build the Internet as you know it are Internet users, too... not all of us are out to milk every last cent from a "freeloader's" visit.
I'd like to note that good ads are mutually beneficial. There are three key parties involved with an ad: the advertiser, the publisher, and the end-user. With a good ad, the advertiser reaches end-users highly relevant to them via the publisher. The publisher receives a fair payout from the advertiser for their work in rounding up their particular group of end-users and allowing the advertiser to communicate with them.
The end-users are informed of something that is relevant to them (it better be if the advertiser has paid to communicate to them), and if the match is right, the ad purchase generates enough new interest in the advertiser's wares to offset the cost of the ad.
In a good ad deal, everyone wins!
Between the three types of ad you brought up, Wind Chaser, I'm inclined to pin anything with autoplaying audio as the worst. It crosses the line when an audio ad begins playing minutes after a page has loaded - often while you're on another tab. Cue a frantic game of whack-a-tab to find the offender and shut it down. Ads like that, which depend on making their presence known when least expected, are more annoying than helpful.
Popups in the traditional sense - literally spawning a new browser window - have largely faded in popularity in favour of on-page "modals"; these are panes/overlays that appear within your open page, usually covering up content and sometimes darkening the screen. While they can border on the annoying, there are legitimately good ways to design an ad like this and integrate it into the natural experience of browsing a particular site. For instance, if I read several articles on a blog, I might actually find an obvious "hey, it looks like you like our stuff - why not subscribe to our email newsletter?" callout helpful and enticing at some point.
I do not recall specific examples, but in recent memory, I'm under the impression that a "hover timer" has become more commonplace - where you actually have to hover over the ad for some length of time before it grows across the page. A poorly built hover ad combines the worst elements of popups (covering your content in a way that makes you rage) and autoplaying audio (unforgivingly forces your attention onto it), but I haven't run into enough of them recently to feel I've been very bothered by them.
A tangent on who's to blame for this very discussion follows:
I've laid out my full stance on this in the thread I linked above, but to complement that, I wanted to add a few notes:
It's incredibly common, especially for smaller sites, to completely outsource the sales and placement of their advertising to one or more services like Google AdSense (the one you've probably heard of), PulsePoint, Chikita, TribalFusion, or others.
These advertising networks don't give site operators direct control over the ads they serve - this is necessary for them to function.
These networks also typically require site operators to literally inject code from their servers into their websites, completely and fully trusting the network to not destroy what the site's users see - again, this is necessary for them to function.
Ad networks are ridiculously convenient.
Ad networks don't pay anywhere nearly as much as direct advertising deals.
Direct advertising deals tend to work out really well because the advertiser and site operator explicitly and mutually agree to show the advertiser's content on the operator's website. This means, ads that generate more conversions, make more money for the site, and are more relevant to the site's users - everyone wins!
Due to various reasons, direct advertising deals tend to be well out of reach of the Internet's smaller sites.
Ad networks are ridiculously convenient, assuming you trust them to not destroy your site and can live with the lower payouts - get an account, paste some code, wait for the cheque.
Sites that depend largely on ad networks for their income find themselves between a rock and a hard place when the networks they trust employ more aggressive means of presenting ads - the operators have no direct control over this, as the networks have unfettered access to what users see.
Smaller networks often pay even less. Trying new networks can be risky, depending on how thin a site's margins are.
There is a widely accepted mentality that Internet-based services and content should be "free".
Nothing is truly free. If you're not paying for it, you're usually the product.
Properly implemented ads can solve the issue by providing what is essentially highly relevant content to the right people.
Properly implementing ads in a way that benefits everyone involved is not a simple problem to solve.
Ad networks are ridiculously convenient.
There is a school of thought that massive ad networks like AdSense did something to democratize the Internet in that they made it possible for just about anyone to sell some space on their site to an automated system and collect some pocket change for it - with a little luck, it'll be enough to pay for the site's online existence... but that's only one way to look at it.
The payout is comparatively abysmal before you get into millions of pageviews (hence, ad-funded websites are often "optimized" to generate more of them by splitting articles across multiple "pages" or otherwise artificially making you load more pages), but there are few other options that consistently generate revenue online when it being "free" is a fundamental part of its purpose.
Did I mention ad networks are ridiculously convenient? More thoughts here.