Yeah I feel for you. I got my account hacked before the 3-day head start was even over. Took about a week to get it back and luckily nothing was taken. In fact, I gained 3 levels and about 20 silver lol.
I know for a fact my email/password was obtained from the Battle.net hack a few months back. I haven't played WoW in almost three years, so when I heard they got hacked I didn't really think much of it. But out of habit I used the same email for my account and the same password. Unfortunately, at the time ANet's email verification thing wasn't working, so I couldn't use that either. After I got my account back I made a new, much harder password, changed my email password (same account), made sure all my passwords were unique (no account sharing a password) and did the email verification, because that was up by then.
If you haven't done the verification, I'd highly recommend it. Basically, ANet (or NCSoft, not sure) records your ip range and location when you log into the verification system the first time. You can choose to set it to remember the location or not. I chose yes. I sometimes play at my bro-in-laws and I have to verify my login from there too. And, if you play from several locations you can actually set it to remember all of them if you want. After this, even if someone else has your login/password, ANet sends you an email to allow or deny the connection. So basically, any unauthorized login attempt would also have to have access to your email account to make it into your GW2 account.
Now, if you've done all this and still got hacked, then you have a much worse security breach than just a game account. For someone to have access to all of this, means you most likely have a keylogger like someone suggested already. And the fact that this has happened twice now, may support this as well. Getting rid of those can be tricky, and talking to some friends who work in computer security, your best bet is a full system reformat and reinstall. Just to be safe.
Lastly, I'm going to include a few links here for password strength testing. There is always the possibility that your account password was just too easy to guess. The first link shows a bit of the technical side of password testing, and the second gives estimated times it would take for someone to guess it. I found them both on Symantec's website so I'd assume they are safe. However, I would just use them as a guild to understanding what makes a password stronger. I'm somewhat paranoid now, so I refuse to put my actual passwords in ;)
http://rumkin.com/tools/password/passchk.php
http://howsecureismypassword.net/
Good luck!