I have 40GBs worth of apps on my iPad 3, and luckily I successfully managed to JB my iPad 3 WiFi without restoring from iTunes (woulda been a major hassle to reinstall everything). Here's what I did:
First I deactivated the passcode. Then I ran Absinthe 2.0 from my Win7 machine. After clicking the jailbreak button, it hung there for like 8 mins 1/4 through the bar, then I got an error saying "application has stopped working". In other words, Absinthe crashed. In the meantime, nothing changed on the iPad screen. It remained on the homescreen.
I closed it, right clicked on the Absinthe icon, went to properties, and checked the Windows XP compatibility mode and Run As Administrator. I fired it up again, and at first it said that the JB has previously failed on the device. It proceeded to recover the files and clear up the previous JB, then it started over. It took like 12 mins, and eventually the iPad restarted, and I was greeted by a Cydia icon on the springboard 🙂