I'm a charter member of ebay and have been using them for 10 years now. I've conducted probably 1000 transactions over the years although my feedback does not reflect that as I refuse to be held hostage to feedback-first-for-reciprocate requests.
Other than the occassional problem with individual buyer/sellers, which you would expect because you ARE doing business with primarily individuals and not Walmart, I have had virtually no issues with ebay (or paypal for that matter) as a company. That being said, I should mention that I've probably also received 1000 emails that appear to be from ebay but which aren't really. If any one of those emails were responded to (or links followed), no matter how official looking, my account would have been hijacked.
Because it is now after the fact, no one can say definitively whether you inadvertently followed an email link or other link while browsing to a site that "appeared" to be an official ebay site but suffice it to say that somehow, a malevolent site captured your username/password combo. Based on my experience and your symptoms, I am going to say that this is NOT an ebay problem but a seperate issue that you have which deserves further looking into.
The fact that your email account AND eBay account AND paypal account were compromised is a clue that perhaps you should investigate spyware or virus activity on your own computer (or another one on your network). The reason is because presumably, all your accounts have UNIQUE passwords and ebay, paypal, and hotmail does NOT know or store the passwords to those other accounts. Contrary to perception, even though paypal is owned by ebay, ebay does not store paypal passwords. In fact, when you pay using paypal after a successful auction bidding campaign, you are still prompted to enter your paypal password. Even if someone was able to login to your ebay account, they would not be able to access your email or paypal account without knowing all of those passwords. So the possible areas to consider as the source would be the password storing services (such as those offered by microsoft and google, i.e. passport), your own computer probably stores your user/password info and spyware, virus or other such hack could phone home on regular basis or otherwise allow a remote user to control your computer.
At the very minimum, I recommend that you install the ebay toolbar and take advantage of ebay's account guard. This feature has a little shield on your toolbar that is green when you are on an official ebay or affiliate (paypal) site but turns gold when you are on any other site. This will be a big help and gives you peace of mind that the ebay site you think you are perusing is actually THE official ebay site.
Good luck and hope this info helps.