Here are the procedures:
1. Launch
iPhone Explorer or Use
SSH (e.g. Cyberduck for Mac or WinSCP for Windows) to access the file system of your jailbroken iPhone/iPad/iPod Touch
EDIT: I would recommend Diskaid instead for Mac users. Much easier and better.
2. Navigate to /var/lib/apt/lists and delete all files under this folder except the “partial” folder
3. Navigate to /var/lib/dpkg/updates. If there is any files inside, please also remove them.
4. Reboot your iPhone/iPad/iPod Touch.
Once booted up, you should be able to launch Cydia properly.