Use the Raster Calculator to average the three bands (with a "+1" so you don't get a divide by 0 error); you can do more advanced averaging if you want of course:
(raster_name@1 + raster_name@2 + raster_name@3 + 1) / 3
This results in a single band output. It supports all output formats that QGIS does, I don't see JP2 on the list, but I didn't look that hard.
ArcGIS: Same premise as QGIS; you'll need the Spatial Analyst Extension to get the Raster Calculator. Looking at it though, ArcGIS doesn't make it as easy to get access to bands via the calculator (its poorly documented, but see here: http://forums.arcgis.com/threads/35761-ArcGIS-10-selecting-attributes-from-multiple-bands )
In ArcGIS 10 Raster Catalog, use full catalog path names instead of
layer names in the expression.
(("C:\Test\KALI-1415.jpg\Band_1") <= 50) &
(("C:\Test\KALI-1415.jpg\Band_2") >= 120) &
(("C:\Test\KALI-1415.jpg\Band_3") <= 173)
*KALI-1415.jpg is my example image.
FME: You didn't ask for this one, but as its available under a free evaluation license. Easy to do, can also do all of the mosaicing and stuff but I guess you've done that. Its either RasterInterpretationCoercer or RasterBandInterpretationCoercer.