Just want to make sure I haven't missed any...
The times Sam voluntarily leaves Dean (as in he makes a conscious, un-supernaturally affected choice to take a break or do something by/for himself). And same for Dean...
1. To go to college
2. Scarecrow - to look for John
3. Hunted - to find answers about himself/"special" children
4. Good God Y'All - to straighten himself out after the demon blood addiction
5. Swan Song - to save the world/redeem himself
6. Slash Fiction - when he finds out Dean killed Amy.
1. Pilot - at Sam's request (not sure if that counts)
2. Time is on my side - to chase a lead when Sam wants to stay.
3. The End...Hmmm, not sure if this counts. He chooses not to get back together with Sam after Sam tells him he wants back in.
4. 99 Problems - leaves to say yes to Michael
5. Blood Brother...Hmm... only leaves to help Benny, not leaving for good, though does leave to do something for himself.