I would also sprinkle some semicolons after the Print commands:
(*Create empty lists*)xlist = {}; ylist = {}; zlist = {};
(*Take inputs for ECEF*)(Label[startinput];
x = Input["What is the x coordinate?"];
y = Input["What is the y coordinate?"];
z = Input["What is the z coordinate?"]; AppendTo[xlist, x] ;
AppendTo[ylist, y]; AppendTo[zlist, z];
(Label[errorcontrol];
again = InputString["Enter more coords? Y for yes, N for no"];
If[again == "Y", Print["Okay!"]; Goto[startinput]];
If[again != "N", Print["Sorry, this is an invalid input here!"];
Goto[errorcontrol]]; If[again == "N", Print["Okay."]]));
(*Debugging*)
Print[xlist] Print[ylist]; Print[zlist]; Print[x]; Print[y] ; Print[z];
(*Put in Coordinate Form*)GeoPositionXYZ[{x, y, z}, "ITRF00"];
(*Convert to LLA*)GeoPosition[%]
(*Display Map*)GeoGraphics[GeoMarker[GeoPosition[%]],
GeoRange -> "World", GeoProjection -> "Robinson"]
(*Display 3D Plot*)ListPointPlot3D[{{x, y, z}}]
