How to I protect my jailbroken iPhone/iPod Touch/iPad?
On a general level, I'd personally secure a jailbroken phone by re-enabling the code signing restrictions of iOS, ensure sandbox requirements are upheld and turn off all remote access. Furthermore, disabling all root accounts and choosing secure passwords for all remaining accounts that your specific jailbreak process creates or modifies would be prudent. 

Apple has teams of people to police third party apps, set up sandboxes, audit security, etc… When you jailbreak, you take responsibility for all of those activities which carries a large technical burden to know what to check in the first place and then how to secure things.

At some point, this exercise becomes a bit metaphysical  - Do you trust Apple to engineer and watch the device? Do you trust yourself to be up on securing unix systems (Practical Unix and Internet Security, 3rd Edition is a fabulous book)? Do you trust the jailbreak to document what changes it has made and allow you the control over security you desire?

There are clearly times when a jailbroken phone (in the hands of a knowledgable operator) can be more secure than Apple's current iOS if it patches a vulnerability that you need to have closed now and not when Apple patches it - but for most, sticking as close to Apple's configuration as possible is the best plan from a security stance.