#These directories may be excluded:

.gvfs                           # contains mounted file systems?
.local/share/gvfs-metadata
.Private                        # contains the actual encrypted home directory
.dbus                           # session-specific
.cache
.Trash                          # do I need to say more?
.local/share/Trash
.cddb                           # cached info about audio CDs
.aptitude                       # cached packages lists

#Flash-specific:

.adobe                          # Cache for flash, maybe others?
.macromedia   # except for Flash persistence, there is no reason to keep this

#Files:

.xsession-errors            # contains errors from the current graphical session
.recently-used              # recently used files
.recently-used.xbel
.thumbnails
.Xauthority                 # session-specific
.ICEauthority
.gksu.lock
.pulse  # directory
.pulse-cookie
.esd_auth

#KDE specific:

.kde/share/apps/RecentDocuments # Recent documents on KDE
.kde/share/apps/klipper         # Contains a history of the Klipper clipboard (KDE)
.kde/share/apps/okular/docdata  # you will loose saved scrolling positions of PDFs
.kde/share/apps/gwenview/recentfolders
.kde/share/apps/kmess/displaypics  # cached other users' profile pics
.kde/share/apps/kmess/customemoticons  # cached emoticons of others

#Firefox-specific (see also Profile folder):

.mozilla/firefox/*/Cache
.mozilla/firefox/*/minidumps    # in case Fx crashes dumps will be stored in this
.mozilla/firefox/*/.parentlock       # session-specific           
.mozilla/firefox/*/urlclassifier3.sqlite  # phishing database, recreated
.mozilla/firefox/*/blocklist.xml   # blacklisted extensions
.mozilla/firefox/*/extensions.sqlite  # extension database, recreated on startup
.mozilla/firefox/*/extensions.sqlite-journal
.mozilla/firefox/*/extensions.rdf
.mozilla/firefox/*/extensions.ini
.mozilla/firefox/*/extensions.cache
.mozilla/firefox/*/XUL.mfasl     # cached UI data, recreated
.mozilla/firefox/*/XPC.mfasl
.mozilla/firefox/*/xpti.dat
.mozilla/firefox/*/compreg.dat

#Opera-specific (related question on Superuser.com: Is documentation available on files and directories in the Opera profile folder?):

.opera/temporary_downloads
.opera/cache
.opera/thumbnails
.opera/opcache
.opera/icons
.opera/application_cache
.opera/widgets/*/cache
.opera/lock

#Komodo Edit:

.komodoedit/*/codeintel/db
.komodoedit/*/host-*/*/codeintel
.komodoedit/*/XRE/Cache
.komodoedit/*/XRE/.activatestate/komodo edit/Crash Reports
.komodoedit/*/XRE/.activatestate/komodo edit/*/Cache
.komodoedit/*/XRE/.activatestate/komodo edit/*/minidump
.komodoedit/*/XRE/.parentlock
.komodoedit/*/XRE/extensions.rdf
.komodoedit/*/XRE/extensions.ini
.komodoedit/*/XRE/extensions.cache
.komodoedit/*/XRE/XPC.mfasl
.komodoedit/*/XRE/XUL.mfasl
.komodoedit/*/XRE/xpti.dat
.komodoedit/*/XRE/pluginreg.dat
.komodoedit/*/XRE/compreg.dat
.komodoedit/*/XRE/*.sqlite-journal
.komodoedit/*/pystdout.log
.komodoedit/*/pystderr.log
.komodoedit/*/history.sqlite.bak
.komodoedit/*/running.lock
.komodoedit/*/mutex.lock
.komodoedit/*/*.xmlc
.komodoedit/*/startup-env.tmp
.komoeoedit/*/commandments.fifo
.komoeoedit/*/history.sqlite

#GnuPG:

.gnupg/rnd
.gnupg/random_seed
.gnupg/.#*
.gnupg/*.lock
.gnupg/gpg-agent-info-*

#Google Chrome:

.config/google-chrome/Default/Local Storage
.config/google-chrome/Default/Session Storage
.config/google-chrome/Default/Application Cache
.config/google-chrome/Default/History Index *

#Other apps:

.pulse/icons                  # Pidgin
.java/deployment/cache        # Cached applets
.icedteaplugin
.icedtea
.gnome2/epiphany/favicon_cache