I have never deleted cookies in my entire life. But that's me. Most spyware removal programs and antivirus programs will quarantine all parts of the infection -- so I don't think a cookie related to a Trojan horse or virus is going to stand much chance of returning to your system if it has been properly cleaned. I was under the impression that a cookie leftover from an improperly cleaned infection could result in some issues and complications, but if you run Norton or McAffee or AVG along with AdAware and SpyBot or whatever -- your cookies should be fine. For me, the hassle of having to enter website info over and over again isn't worth it. Of course, cookies can be manually removed on an individual basis, but this is time-consuming, going through the list and figuring out what's what.
I'll agree that I'm doing fine with Windows 98 for now, though the fact is that it IS an unstable OS, always has been. If I had the cash to get a new PC, I'd do it tomorrow. I get a blue screen about every two days, and Explorer crashes almost daily. Admittedly, though: I seriously push my system beyond its limits. I run software and hardware that is not supposed to work with my meager processor.
Here's a final tip if you find that your antivirus software tells you that you cannot remove certain infected files: just boot into Safe Mode (press F5 at Windows startup). This loads minimal drivers and startup files (your screen will look awful, just continue on anyway). Rescan with your virus software in Safe Mode. The files will probably be able to be removed at that point. Then reboot normally.
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