I have a cutting that I had been trying to root.  It rooted very well in a cup and I have been seeing roots for 2-3 weeks now but have yet to see any leafing.  I realized last night that the reason I have not seen any leafing is because I have the cutting in upside-down.  I know... rookie mistake.  Now I am wondering what i should do?  Do I simply pull the cutting out and bury the entire thing right side up and hope that shoots grow out of the ground??? 

You could do that, and it would probably work.  In my experience, if the cutting is healthy, it will send up a shoot and be just fine.  Trees grow in "U"s all the time, above ground and under ground.  It can live with a small section upside-down if it must.  I have a 6 foot 160-50 that was upside this time last year and I never flipped it.

It's more about the amount of time it will take for the cutting to orient itself. Eventually it will leaf out. 

The problem with cuttings is that it will eventually run out of energy.  Unless there are functioning leaves when it runs out of energy it dies.  It will take longer to get leaves in the sun if it's upside down.  

If there are no shoots yet I'd turn it right side up but that's just my opinion.  If there are good roots I'd also give it some houseplant strength fertilizer.

I just looked at it and a leaf is starting to pop out above the soil line, which in this case, is really on the wrong side of the roots, if that makes any sense at all, haha.
I think I will go home and flip it over

BUT

Should I be cutting the cutting that is above ground now and just be flipped and uppotting the root ball or should I be burying the entire 5 " that is currently above ground?

When this topic comes up someone always chimes in and says "replant it sideways",well this time it's me!,I made this rookie mistake late last summer,it rooted nicely then went dormant, this spring when it woke up it pushed out buds upside down!, one of those 'ah crap' moments in life,I took it out the pot and reported it sideways in a wide pot at a bit of an angle,barely covered and with the buds angled upwards,keeping one just visible,now it's pushed out not 1 but 2 growing stems and started leading out.

Whatever choice you make good luck!

I did that also took a long time but sent leaves up. When I up potted I burried the cutting sideways.