Get GDAL (the simplest installs are either from GISInternals or OSGEO4W). Then use the "gdal_translate" utility from the command line or a batch script. Command line example: for %i in (C:\inputdir\*.bil) do @gdal_translate -co 'COMPRESS=LZW' %i C:\outputdir\%~ni.tif
This will preserve the colour table. The -co 'COMPRESS=LZW' will use LZW lossless compression for the output tif.And here's a batch file to do the same, but recursively over subfolders and preserve the folder hierarchy: (note, the previous one liner will work from a command prompt, if you want to use it in a batch file, change the "%" symbols to "%%").@echo off
cd /D C:\inputdir
for /R %%i in ("*.bil") do (
mkdir "C:\outputdir%%~dpi"
gdal_translate -co "COMPRESS=LZW" "%i" "C:\outputdir%%~dpi%~ni.tif"
)