This is a phrase largely equivilent to fucked up or screwed up. It roughly means "in a state of disarray" and is commonly used in the phrase "to jack someone/something up". In some cases, the meaning may be slightly altered by the fact that to get "jacked" can mean to be struck or injured.
That's jacked up man. I can't belive your girlfriend is cheating on you.
I got in a wreck last night. My car got totally jacked up.
1. not working properly or as intended.
2. having used a large quantity of speed, cocaine, or other amphetamine.
3. cut or lacerated by means of a make-shift knife or blade. see SKIV
4. In generally poor or injured condition.
sense "1": "This is so JACKED UP! She said she'd be here at eight!"
sense "4": "I want to play, but my shoulder's still JACKED UP from last weekend.