Disk Protect v2.1 for GEOS by Rober L. Thaller (Released 9/16/1988) is a utility that will let you change a disk into a Master or Boot disk, making it impossible to delete files from the DeskTop.  It also works the other way around.

This program was found on issue 10 of "Disk O' Quarter" put out by the Commodore Users of Wichita.

Drive Cleaner v2.0 by Jorgen Eckel (Dated 8/15/1990) is a utilitiy for GEOS 128 (80 Columns) that will assist in cleaning the heads on a floppy drive using a special cleaning disk.  Although this version says it's specifically for the Commodore 128 version of GEOS, it works fine on GEOS for the Commodore 64 if you don't mind a few of the dialogue boxes not looking quite right as you can see in the screenshots.  

Full documentation is included in English even though the program itself is German.  Don't let the German scare you off, it is quite intuitive to use without being able to read the button labels.

geoDiskEdit 128 v1.0 by Mike Craig (Dated 4/16/1989) is a fully featured track & sector editor for GEOS 128 in both 40 and 80 column mode.  As an interesting side note, this was programmed with geoCope.

GEOS Busters by Kracker Jax Protection Busters is a utility written for GEOS and the Commodore 64 that will remove the protection from GEOS 64, GEOS 128, Graphics Grabber, GEOdex, GEOWrite 64 & 128, GEOfile 64 &128, GEOcalc 64 & 128, GEOspell GEOMerge, GEOPublish and GEOProgrammer.

The program must be run from inside GEOS, but contains full built-in instructions.