libguestfs is a set of tools for accessing and modifying virtual machine (VM) disk images. You can use this for viewing and editing files inside guests, scripting changes to VMs, monitoring disk used/free statistics, P2V, V2V, performing partial backups, cloning VMs, and much more. libguestfs can access nearly any type of filesystem including: all known types of Linux filesystem (ext2/3/4, XFS, btrfs, etc.), any Windows filesystem (VFAT and NTFS), any Mac OS X and BSD filesystems, LVM2 volumes, MBR and GPT disk partitions, raw disks, qcow2, CD and DVD ISO images, SD cards, and dozens more. libguestfs doesn't need root permissions.
FSlint is a toolkit to find various forms of lint on a filesystem. At the moment it reports duplicate files, bad symbolic links, troublesome file names, empty directories, non stripped executables, temporary files, duplicate/conflicting (binary) names, and unused ext2 directory blocks.
BleachBit deletes junk to recover disk space and maintain privacy. It rids your system of old junk including cache, Internet history, temporary files, unused locale files (better than localepurge), logs, and cookies. Designed for Linux systems, it wipes clean 50 applications including Adobe Reader, Bash, Firefox, Flash, OpenOffice.org, Opera, Real Player, Skype, and more. It shreds files so that they cannot be recovered, and it wipes free disk space to hide insecurely deleted files. It offers both a simple PyGTK GUI and a command line interface for automation.
trash-cli is a command line interface to the FreeDesktop.org trashcan. It implements the FreeDesktop.org trash specification. For each trashed file, it will remember the name, original path, date of deletion, and permissions. It interoperates with KDE and GNOME Trash, and is CLI compatible with the rm command.