I came across Stop pop-up ads and adware in Safari. Since many people have been afflicted with some of this stuff, it has good ways to clean out the crap.

Wouldn't a faster and easier solution be to use Adblock Plus?
There is a version available for Safari.

From their website:
Adblock Plus is a free extension that allows you to ... block annoying ads, disable tracking and block domains known to spread malware. ... Adblock Plus is an open source project.
Available for Android, Chrome, Firefox, Internet Explorer, Maxthon, Opera, Safari and Yandex, Adblock Plus uses filters that you choose to block all unwanted elements.
Adblock Plus itself has no functionality; it doesn't block anything until you "tell" it what to block by adding external filter lists. Filter lists are essentially an extensive set of rules that tell Adblock Plus which elements of a website to block. You can add any filter list you want. For example, block tracking or malware. You can also create your own filter lists. Almost all filters are open source, therefore many filter lists have been created by Internet users.

I use AdBlock along with Ghostery, which is also a free, Safari Extension. Here's a link to what it does, etc. Ghostery FAQ

The combination of these 2 Extensions provides ad blocking and defeating web servers being called by a particular web page.

Ghostery provides a temp window showing called web servers; it's amazing to see how many servers are being called. 99% of the time, I'll subsequently click on Ghostery to set that server to Off. ...I haven't sensed any noticeable speed drop-off, on the desktop Extension, due to Ghostery doing its tasks.

Lastly, I haven't found any login issues with any of my banking and investment sites, even though both are working in the background.

Ghostery interferes with a few sites that I log into and have to pay bills online. Mostly, it doesn't. So, I disable it temporarily, as necessary. (I also have AdBlock.)

Ghostery does allow specific, web servers, for specific sites, be toggled Off for preferred site access.

Just as an example, 1Password's Forum (AgileBits) uses Avatars (via Gravatar), and I toggle Gravatar Off just so I can see the Avatars the Forum is using. ...So, there's flexibility in what one allows.

Ghostery allows sites to be permanently white listed so they don't have to be toggled.

AdBlock, aside from blocking pop-ups, has a wonderful feature that allows you to block any html element...FTM's masthead, the multitude of screen-cluttering junk that eBay and Chase Bank constantly deliver, etcetera, etcetera, and so forth... Click, and they're gone!!!

As PbGuy already mentioned about Ghostery, instead of allowing all trackers on a site by whitelisting it (and kind of throwing out the proverbial baby with the bathwater), you can also allow just the problem one(s) for that site* only. Of course, you'll have to know which tracker is the crucial one to allow, but that's relatively easy to establish, particularly if there are only a few trackers on the site (allow tracker and reload page). If you're a frequent site visitor, it may be worth your while to check them all even if there are more than a few.

If you're also using Little Snitch and/or an adblocker, note that they may be involved in your problem too. When testing the various trackers on a site, you might want to disable those utilities temporarily, unless you're absolutely sure they are not part of your problem.

*) To allow a particular tracker for the current site, click the rightmost button behind the tracker's name in Ghostery's (v.5.x) listing. The toggle is to the left of this button. Hovering over a button will bring up a tooltip explaining the button's action.

You're correct of course, and I should have explained myself.

This whole internet privacy thing reminds me of being cheap.

To be truly cheap, you can't place any value on your own time, and to achieve maximum internet privacy you've got to fall into a similar mode.

I very rarely visit a site that gives me problems, but when I do, there's so much potential toggling to do(*), not to mention the fact that the culprit may be an entry in my hosts file, that if I can immediately establish that Ghostery (in general) is at the root of my problem I find it most convenient to simply whitelist the site and give up whatever it costs in terms of information. The time for info trade-off is well worth it to me, particularly in view of the infrequency with which I have to make it and the benign nature of the sites involved.

(*) I toggled individual trackers in Ghostery until I ran into a situation in which I had to toggle more than one, and it was that particularly frustrating episode of permutations and combinations that drove me to simply whitelist entire sites.

Hi, I'm tagging on to this thread as it is similar to the question I'm about to ask.

I've had Adblock Plus installed for years (so it's not that).

Recently I was on a health/medical website in, AFAICS, America (I'm in the UK). Reading down the page, I was astonished to find the text interrupted with a clickable link to a "sponsored site" which was a bed+breakfast location in UK, which I had previously clicked on/looked at. There is absolutely no way that B+B could be "sponsoring" a health website which is America-based.

The next time I found myself - exploring a medical issue - on that website, my reading was again interrupted with a hotel site I'd recently visited on booking dot com.

Checking my plug-ins, I found a "google analytics" which Firefox sternly told me was not recommended. I disabled, removed it, restarted Firefox. I've also cleared cache and history. I'm not about to revisit that USA health website to check my theory ....> was google analytics the culprit?

Most likely. It was not so much the site you visited, as the cookie trail you left behind that allowed the "sponsored" ad to appear.

I have had similar experiences on the most innocuous sites where I see ads related to where I previously have surfed. Welcome to the World Wide Web!

"C" is for cookie, and that's good enough for me

http://abcnews.go.com/images/Entertainment/gty_cookie_monster_dm_120525_wblog.jpg

I used to use something called Flush to get rid of Flash cookies. I just looked at the script and it is thus:

tell application "Terminal"
activate
do script "ls -R ~/Library/Preferences/Macromedia/Flash*Player | grep -v settings | grep -v preferences | grep .sol | cat -n"
display dialog "Welcome to Flush 3.1. Do you want to flush these flash cookies into your Trash now?" buttons {"Not Now", "Flush Away!"} default button 2
if button returned of result = "Flush Away!" then
set fileToDelete to (((path to preferences folder) as text) & "Macromedia:Flash Player") as alias
tell application "Finder"
delete fileToDelete
end tell
end if
quit
end tell