If you want to skip x values between xmin and xmax, and y values between ymin and ymax you can do a conditional plot:
splot "input.dat" u 1:4:( $1 >= xmin && $1 <= xmax && \
$4 >= ymin && $4 <= ymax ? 1/0 : $8 ) w pm3d
The code above tells gnuplot to ignore the points outside of range.
For instance, I generate the following random data with bash:
for i in `seq 1 1 100`
do for j in `seq 1 1 100`
do echo $i $j $RANDOM >> input.dat
done
echo "" >> input.dat
done
And now tell gnuplot to ignore a certain region:
xmin = 25; xmax = 36; ymin = 67; ymax = 88
set view map
splot "input.dat" u 1:2:( $1 >= xmin && $1 <= xmax && \
$2 >= ymin && $2 <= ymax ? 1/0 : $3 ) w pm3d not

If you have multiple regions that you want to skip simply use an "or" logical operator || to delimit areas:
xmin1 = 25; xmax1 = 36; ymin1 = 67; ymax1 = 88
xmin2 = 50; xmax2 = 90; ymin2 = 23; ymax2 = 34
set view map
splot "input.dat" u 1:2:( \
($1 >= xmin1 && $1 <= xmax1 && $2 >= ymin1 && $2 <= ymax1) \
|| \
($1 >= xmin2 && $1 <= xmax2 && $2 >= ymin2 && $2 <= ymax2) \
? 1/0 : $3 ) w pm3d not
