ListPlot under conditions

Different approach:

list = Import["nb.txt", "Table"]

lim = .0001;
c1 = # > lim && #2 == 0 &;
c2 = # <= lim && #2 == 0 &;
c3 = # > lim && (MemberQ[{1, 2}, #2]) &;
c4 = # <= lim && (MemberQ[{1, 2}, #2]) &;

An array with indicators if given record fulfills given condition:

cond = Outer[Apply, {c1, c2, c3, c4}, list[[ ;; , {-2, -1}]], 1] 

ListPlot[Pick[list[[ ;; , ;; 2]], #] & /@ cond, 
         PlotStyle -> {Orange, Red, Green, Blue},
         BaseStyle -> Directive[AbsolutePointSize@10]]

Edit

 ListPlot[Pick[list[[;; , ;; 2]], #] & /@ cond, 
          PlotStyle -> {Orange, Red, Green, Blue}, AspectRatio -> Automatic,
          BaseStyle -> Directive[AbsolutePointSize@3], 
          PlotMarkers -> "\[FilledSmallSquare]"]

It seems your data is an equally spaced array with dimensions:

Length /@ (Union /@ (list[[ ;; , {1, 2}]] // Transpose))

{109, 109}

I'm going to post the code, some explanations will appear this evening. This is my approach to plot colored plane with not points overlapping.

data = Table[, {109}, {109}];
colordata = Table[RGBColor[0, 0, 1], {109}, {109}];

g = Which[# > lim && #2 == 0, Orange, 
          # <= lim && #2 == 0, Red, 
          # > lim && (MemberQ[{1, 2}, #2]), Green, 
          # <= lim && (MemberQ[{1, 2}, #2]), Blue] &;

(data = ReplacePart[data, IntegerPart[(.55 + #) 100] -> 1]) & /@ list[[ ;; , {1, 2}]];

(colordata = 
 ReplacePart[colordata,
            ({110 - #2, #1} & @@ IntegerPart[(.55 + {#[[ 1]], #[[ 2]]}) 100]
            ) -> #[[ 3]]]
) & /@ ({#, #2, g[##3]} & @@@ list[[;; , {1, 2, -2, -1}]]);

ListPlot3D[data, VertexColors -> {colordata}, Mesh -> None, Lighting -> "Neutral", 
                 ViewPoint -> {0, 0, 1000}, ImageSize -> 500, Axes -> False]

If you are not concerned by the particular color order or choice, as your conditions partition your data you could use GatherBy[]. Let your data be in variable data. You could use:

gather=GatherBy[data,{#[[-2]]<=0.0001,#[[-1]]==0}&];
ListPlot[#[[All,{1,2}]]&/@gather,PlotStyle->{Orange,Red,Green,Blue}]

The gather will partition your data into the 4 possible outcomes sorted depending on how data is sorted/unsorted. Obviously you can adjust point size and other options at your discretion.

Using the dataset availablle for download the timing of GatherBy[] was 0.109201 seconds. Using:

ListPlot[#[[All, {1, 2}]] & /@ gather, 
 PlotStyle -> {Red, Orange, Blue, Green}, AspectRatio -> 1, 
 BaseStyle -> {PointSize[0.013], FontFamily -> "Kartika", 12}, 
 Frame -> True, Axes -> False]

yields:

Consistent with question edit (except for coloring and some style aspects)

Here's my approach:
The data is already quantized on a 1/100 grid so I believe we should be plotting it as such.

First Import the data and extract the columns we wish to work with:

data = Import["data_gRC.out", "Table"][[All, {1, 2, 6, 7}]];

Check the ranges of the coordinates:

minmax = {Min@#, Max@#} & /@ Take[Transpose[data], 2]

{{-0.54, 0.54}, {-0.54, 0.54}}

Build a color function (borrowing from Nasser):

fn[f_, 0] /; f <= lim1     = Red;
fn[_, 0]                   = Orange;
fn[f_, 1 | 2] /; f <= lim1 = Blue;
fn[_, 1 | 2]               = Green;
fn[__]                     = Black;

lim1 = 0.0001;

Build an array of colors from the coordinates and fn using SparseArray, first rounding and scaling the coordinates to integer values starting from one (here 55 + 100 x):

sa = SparseArray[Round[55 + 100 {#, #2}] -> fn[##3] & @@@ data];

Do the magic with MatrixPlot:

MatrixPlot[
 Reverse[sa\[Transpose]],
 DataRange -> minmax
]

I might have understood the question in a wrong way, but I would use the ColorFunction Option of Listplot in Combination with a suitable anonymous function to generate the Color depending on the (x,y) coordinates.