Yes, Quarantine is just an extra safety measure. Even the best anitivirus (AV) and other security scanners make mistakes at times--the good ones will correct that quickly, but it still happens.
The thorough scanners will also flag certain files and programs that can be used for either good or ill. Termed Riskware or hacker tools, and vaious other names, they are just bringing the presence of such files to your attention and letting you decide if it is something you are using to troubleshoot or repair a problem, or if it is something installed by a hacker or malware that may indicate an infection.
There are also times when legitimate files that have been infected so holding these files in quarantine until they can be cleaned or replaced insures they are handled properly. Most AV vendors will give you an option of whether or not to clean or delete a file as well as whether or not to quarantine it when found during a scan. This confuses many people. If an AV says a file can't be cleaned, rule of thumb is the file has been added in toto by malicious software and is safe to delete. But the safe course of action is to quaranine the file and investigate whether it is safe to delete or not.
BC has several resources to assist in this: Startup Programs DatabaseThe File DatabaseUninstall Programs Database
Those will cover most files and give you an idea of if they are legit or not or whether they are associated with malware. Still there are some processes that will not appear in startup or those other databases, so another database to check:TASK LIST PROGRAMS at AnswersThatWork
Of course we like to think that the greatest resource of all is the shared knowledge of BC's members, so don't ever hesitate to ask in the forums as you have done.
It is rare tho now for there to be a file that needs to be cleaned. Those are mostly from true viruses, which don't show up much any more. There are still some out there tho, so using quarantine is still the safest course of action.
The problem with leaving files in quarantine is that other scanners will detect those files leading some to believe that they are still infected. As long as you understand that those files have been dealt with and no longer active then you can leave them in quarantine and not worry. It's basically what I do.
But since most of those files are bad in and of themselves, there is no need to keep them in quarantine. Tracking cookies you sure don't need as they keep track of your surfing habits and mostly only enable you to view ads that they think you will be interested in based on those habits. Not a really serious threat or an infection per se, but they won't damage anything if you just delete them and keep them cleaned up.
This is the first time I used Ewido and I think it is a great program!
Yes, ewido is a great program and I recommend you keep it. There is some confusion about the 30 day trial, leading some to believe that it can no longer be used when the trial is up. But there are only a few features that are disabled, such as scheduled updates and background monitoring that are disabled when the trial is up, and ewido will effectively scan and clean as long as you keep it updated manually.
Altho it is now called an antispyware, it is really more of an anti-trojan and even cleans some worms. Along with your antivirus, a firewall and a few anti-spyware apps, you'll have the recommended "layered approach" to security and will be in pretty good shape.
This doesn't mean that malicious software won't still get through. It is common that a well protected machine still gets infected, depending on how much high risk behavior you engage in and some other factors. You didn't mention what other security tools you have installed and use. I would still recommend Spybot Search & Destroy and Ad-Aware in addition to ewdio. The info in the following topic still applies: http://www.bleepingcomputer.com/forums/t/134/how-to-use-this-forum/
And other means of preventing infection are here:
Simple and easy ways to keep your computer safe and secure on the Internet