Reclassify raster values of 9999 to NoData, leaving all other values alone, in ArcGIS Desktop?

you can do this with arcpy, if you want. In this code, any input cell with a value 9999 will be set to NoData in the output raster, and the remaining cells will retain their original value.

import arcpy
from arcpy import env
from arcpy.sa import *
env.workspace = "C:/sapyexamples/data"
outSetNull = SetNull("elevation", "elevation", "VALUE = 9999")
outSetNull.save("C:/sapyexamples/output/outsetnull")

you can read Conditional evaluation with Con and Set Null (Spatial Analyst) from ArcGIS Resource Center...

Syntax
SetNull (in_conditional_raster, in_false_raster_or_constant, {where_clause})

i hope it helps you...

Your approach used to work fine in old versions of Arc but not now. You can around this by adding in another value (set to be identical to the old one). One value is usually sufficient unless you have floating point values, in which case I would add the highest and lowest original values (set to be the same as their original value). The values in between USUALLY end up as per the original.

This is a hack, so always check the results afterwards!