To my knowledge there are currently only three genuine Bf-109s with DB engines, maintained to an airworthy state. Two are Emils, one with the FHCAM museum in Seattle (which is temporarily closed) and the other with the Biggin Hill Heritage Hangar which has yet to make it outside the airfield's airspace in the 4/5 years it's been over here. Also In the USA The MAM in Virginia Beach operate a G-4 that was restored by Meier Motors in Germany a couple of years ago, I believe the number of original parts may be minimal and it flies with a later G-model lower cowling, but is still classed as an original 109.
There is also a genuine Spanish Civil War 109E-1 under restoration in Germany for a UK customer that will certainly be something to see when finished.
As Arthur and Nick confirm, there are a number of Buchons converted to Gustav models that are airworthy or undergoing maintenance/restoration.
In Germany:
The Hangar10 collection on the island of Usedom operate a G-6, a merlin powered two seat G-12 (that has flown with a DB) and a G-14.
The EADS Messerschmitt Flugmuseum operate a G-4 (Red 7 that visited Duxford in 2015) and a G-10, both of which are undergoing maintenance. Their G-6 was also recently fully overhauled.
Hope that helps.