General confusion or disarray:
* Confused
* Disorganized
* Chaotic
* Jumbled
* Tangled
* Bewildered
* Foggy
* Vague
* Unclear
* Cluttered
Specifically for thinking or reasoning:
* Confused
* Disoriented
* Rambling
* incoherent
* Muddle-headed
* Scatterbrained
For physical objects:
* Messy
* Untidy
* Disheveled
* Scrambled
* Mixed up
The best synonym will depend on the specific meaning you want to convey.