Assuming I understood your question correctly, do you really need a palette if you just want to set only a few specific colors to a few specific points?
You are using two plotting styles with points and with labels you can combine them in one plot command.
Code:
### variable color points
reset session
$Data <<EOD
###label x y z
1 244.8 18 6.1
2 248.0 10.4 7
3 294.4 6.3 13.7
4 248.0 7.5 8.92
5 240.0 3.69 6.61
6 240.48 3.69 8.92
7 256 5.7 15.8
8 256 7 10.6
9 256 4.1 8.2
10 256 5.1 12.3
EOD
myColor(col) = column(col)==3 ? 0x0000ff : \
column(col)==6 ? 0x00ff00 : \
column(col)==9 ? 0xff0000 : 0
set key noautotitle
splot $Data u 2:3:4:(myColor(1)) w p pt 7 lc rgb var, \
'' u 2:3:4:1 w labels offset 0.0,0.7,0.7
### end of code
Result:

Addition: (colored labels)
If you want to have colored labels then change the plot command as follows:
splot $Data u 2:3:4:1:(myColor(1)) w labels tc rgb var
Well, you have to decide:
- using only labels it might be difficult to locate the exact position of your data point
- using a point and a label without offset it might be diffcult to read the number
Result: (colored label without point)
