Change the color of a Locator in a Manipulate

Use Appearance->SomeGraphicsObject:

l = Graphics[{Red, Disk[{0, 0}, .1]}, ImageSize -> 10];    
Manipulate[Graphics[{Line[{{0,0},pt}]},PlotRange->2],
 {{pt,{0,0}},{-2,-2},{2,2},Locator,Appearance->l}]

You can use any Graphics or Graphics3D object for this, i.e.:

l = Graphics[{Red, Table[Circle[{0, 0}, i], {i, 3}]}, ImageSize -> 20];

or

l=Graphics3D[{Blue,Cylinder[],Red,Sphere[{0,0,2}],Black,Thick,Dashed,
 Line[{{-2,0,2},{2,0,2},{0,0,4},{-2,0,2}}],Yellow,
 Polygon[{{-3,-3,-2},{-3,3,-2},{3,3,-2},{3,-3,-2}}],Green,
 Opacity[.3],Cuboid[{-2,-2,-2},{2,2,-1}]},ImageSize->50];

As far as I know, you can't change the colour of the default locator directly, but you could use the specification for the default locator to create a coloured version of the default locator. These specifications can be found in the file MiscExpressions.tr located in $InstallationDirectory\SystemFiles/FrontEnd/TextResources. It turns out that the locator is specified as

GraphicsBox[
 InsetBox[GraphicsBox[{col, {AbsoluteThickness[1], 
     Antialiasing -> False, 
     LineBox[{{{0, -10}, {0, -2}}, {{0, 2}, {0, 10}}, {{-10, 0}, {-2, 
         0}}, {{2, 0}, {10, 0}}}], Antialiasing -> True, 
     CircleBox[{-0.5, 0.5}, 5]}, {AbsoluteThickness[3], Opacity[0.3], 
     CircleBox[{-0.5, 0.5}, 3]}}, ImageSize -> 17, 
   PlotRange -> {{-8, 8}, {-8, 8}}], {0, 0}, Center]]

So using this you could create a coloured locator by doing something like

loc[col_] := Rasterize[
  ToExpression@
   GraphicsBox[{col, {AbsoluteThickness[1], Antialiasing -> False, 
      LineBox[{{{0, -10}, {0, -2}}, {{0, 2}, {0, 10}}, {{-10, 0}, {-2,
           0}}, {{2, 0}, {10, 0}}}], Antialiasing -> True, 
      CircleBox[{-0.5, 0.5}, 5]}, {AbsoluteThickness[3], Opacity[0.3],
       CircleBox[{-0.5, 0.5}, 3]}}, ImageSize -> 17, 
    PlotRange -> {{-8, 8}, {-8, 8}}],
  Background -> None]

Graphics[{Disk[], Locator[{0, 0}, loc[Darker[Green]]]}]

You could simply draw the locator with crosshairs. Color of circle, crosshairs and inner disk can be set as desired.

Manipulate[
    Graphics[{Line[{{0, 0}, pt}]}, PlotRange -> 2], 
    {{pt, {0, 0}}, {-2, -2}, {2, 2}, Locator, 
       Appearance -> Graphics[{Black,
           Line[{{0, 1.5}, {0, 3}}],Line[{{0, -1.5}, {0, -3}}],
           Line[{{-1.5, 0}, {-3, 0}}], Line[{{1.5, 0}, {3, 0}}],
           Circle[{0, 0}, 2], Blue, Disk[]}, ImageSize -> 20]}]

---

If you don't require a replica of the default locator and a single color suffices, you might use \[CircleDot] or \[CirclePlus]. For example,

Manipulate[Graphics[{Line[{{0, 0}, pt}]}, PlotRange -> 2], 
  {{pt, {0, 0}}, {-2, -2}, {2, 2}, Locator,  
    Appearance -> Style["\[CircleDot]", Blue, 24]}]