So, I came up with two tools that work together to achieve this. One is called Ad Highlighter which changes the link color on any ads that are using click tracking software. The color changes depending on what software they are using. The second tool is called UnMask URLs. When you click this button on a Google search result and mouse over the link, the actual destination URL will appear as shown in the screenshot below.
Both of these tools are included in my free Firefox Addon called SEM Tools which you can download here.

After installing the Addon, try this search result or this one.

Mousing over the link shows us that Citroen is using DartSearch for tracking.

These tools also work on Yahoo and Baidu. Yahoo and Baidu make it especially hard to show the destination URL but the UnMask tool can still decode these URLs, although it takes a little longer to process.

You can test it on this Yahoo page or this Baidu page. Make sure to click the UnMask URLs button once you get to the page. You don’t need to press the button on Google but it will still work.

After pressing the "Unmask URLs" button we can see that MGMMirage is using Atlas,

If you would like to add or change which advertisers appear, you can edit the list yourself from the Options menu or just send me an email on the feedback page and I can add it to the next version.

To run a pay-per-click campaign it is essential to be able to track when people click on the ad and whether they go on to buy something from your site. What happens after clicking the ad is called post-click tracking and this is the basic technology that all SEM campaigns need.
We can divide companies up into three groups based on the the type of post-click tracking software they use as follows:
1) Search Engine’s own tracking software
2) Third-party tracking software
3) In-house or Proprietary software

1) Search Engine’s own tracking software
Google, Yahoo and Microsoft all provide their own tools and software to track post-click sales. If you have a small site/budget or you work with a small agency then this is a common choice. Google’s system integrates with Google Analytics so this makes implementation easier.

Pros:

• Cost- No extra cost for using their software.
• Integration- The software is integrated with the click data so all the data is in the same place.

Cons:

• Compatibility- Difficult to use the same tracking across multiple search engines.
• Data Ownership- All your data is owned by the same company that is selling you the ads.

2) Third-party tracking software
Companies like Doubleclick (Google owned), Atlas (Microsoft owned) and Clickable (independent) provide access to their software on a self-serve basis. The payment system varies but often it is based on cost-per-click. These systems are popular with cross-media agencies as they are often connected with tracking systems for display advertising.

Pros:

• Compatibility- Using the same system across multiple engines is one of the big selling points for these companies.
• Data Ownership- The data is not owned by the search engines.
• Added extras- Often you will get advanced features that aren’t supported by all the engines.
• Cross-media Tracking- Often these systems integrate with tracking software for other media like Display Advertising.

Cons:

• Cost- The price might seem low per click but it can add up to a lot. Depending on the price structure this can be a problem in some verticals (low-margin/low CPC industries).

3) In-house or Proprietary software
Many search engine advertising agencies have their own custom tracking software. This can be a differentiator for these companies. Companies with their own proprietary systems are normally pay-per-click specialists.

Pros:

• Compatibility- Same as in number 2, using the same system across multiple engines is one of the big selling points for these companies.
• Added extras- Many agencies will use their technology to differentiate themselves. This can mean access to advanced features, reporting and other value-adds.

Cons:

• Data ownership- Changing agencies can be an issue as it means changing tracking software. Re-implementation and transfer of data can be an issue.
• Cost- Some agencies will charge a separate fee while some will integrate it into their regular fees.

Summary
So that gives you an idea of the available options. A lot will depend on the goals of your marketing.
Generally speaking, small companies or companies with low budget campaigns will often go with Number 1.
Companies with a large marketing budget across many media often go with Number 2.
Online companies or companies in verticals where search is very important (travel, classifieds etc.) often go with Number 3.
But again, this won’t suit every company or every agency.

If you are looking for a company with their own proprietary system (Number 3), I’ve put together a List of 3rd-party pay per click tracking software.
If you know of other companies and would like to add them to the list then please let me know on the Feedback page.

1) Firstly, get a list of the URLs that you want to check.
If you are checking links from an adwords campaign, open up Google Adwords Editor, go to the keyword or creative tab and copy all the keywords/creatives and their URLs. If you want to check the links on a website, go to the page with the links you want to check and then choose “Get Links” from the toolbar (it’s in the URL Tools drop-down).

Then click the “Copy all Links” button.

2) Now we’ve got our list, open up the Link Checker.
It’s called “Link Checker” and it’s in the URL Tools menu.

Then paste the links from step 1 into the top box.
It’s OK if there is other text as well because the Link Checker will just ignore the extra text.
If you are copying the links from Adwords Editor then check the “Is there a header row?” box to ignore the first line.

3) Run the Link Checker.
Click the “Check URLs” button. Below the button you can see the progress. In the bottom box are the results of the test.
If you copy all the results and paste them into a spreadsheet you can see which links are dead or broken and which are working OK.

4) Replace the broken links in your site/ad campaign.

Bonus:
The results also include the “Final URL“. For most links this will be the same as the original link but if you are using click tracking or other URL redirects, this column will show you the actual page that users land on.

Happy link fixing!