7Gif - http://www.xtreme-lab.net/7gif/en/index.html

Ajax Animator - http://antimatter15.com/wp/ajax-animator/
Alternate Pic View ExeSlide (self executing Slideshows/Gif animations)
 - http://www.alternate-tools.com/pages/c_exeslide.php?lang=ENG&nav_option=111111111
Animation Studio - http://myweb.tiscali.co.uk/tapptoons/animationstudiopage.htm
Animation Viewer (nfohp) - http://www.brothersoft.com/animation-viewer-by-blaiz-enterprises-66929.html
Animator - http://www.angelfire.com/nd/seireg/downloads2.htm
Animator-9 (nfohp) - http://www.brothersoft.com/animator-9-74851.html
AnimGif - http://www.sigord.co.uk/Submits/Software.htm
Anis - http://www.ssec.wisc.edu/anis/

Beez (vector-drawing editor/animator) - http://beez.sourceforge.net/
Blaiz Animator (hpnf) - http://download.cnet.com/Blaze-GIF-Creator/3000-2186_4-10662556.html
Blender - https://www.blender.org/
Bumper (image player) - http://remcodek.home.xs4all.nl/down_tools.html

CaraQ Avatar Maker - http://www.freewarefiles.com/CaraQ-Avatar-Maker_program_33178.html
Clara (online) - https://clara.io/

DAZ 3D (reg req) - https://www.daz3d.com/get_studio
DOM Animator (nfohp) - http://www.freewarefiles.com/DOM-Animator_program_45237.html
DP Animation Maker - http://www.animationsoftware7.com/
Draw SWF - http://drawswf.sourceforge.net/index.html

Falco Gif Animator - http://www.falcoware.com/FalcoGIFAnimator.php
Fickle Animation Generator - http://emogic.com/store/index.php?main_page=index&cPath=10
Framer (1)(image strip) - http://remcodek.home.xs4all.nl/down_tools.html
Framer (2) - http://www.tawbaware.com/framer.htm

GbAnimator - http://www.garybeene.com/free/index.htm
Gif Splitter - http://www.xoyosoft.com/gs/index.htm
Gifted Motion - http://www.onyxbits.de/giftedmotion
GL Animator (nffhp) - http://www.filetransit.com/view.php?id=45689
GLtip (2d -> 3d animation) - https://sites.google.com/site/hkideabrush/gltip
GR44 Animator (LFV) - http://www.321download.com/LastFreeware/page19.html

HL Free Gif Animator - http://freeartsoftware.com/survey3d2d-downloads/download-info.php?sid=466

Imagine (view animations) - http://www.nyam.pe.kr/
Instagiffer - http://instagiffer.com/

JavaScript Animator Express - http://www.nirsoft.net/utils/jsae.html
Jumpwel (html) - http://download.cnet.com/Jumpwel/3000-2186_4-10262585.html

KPedit - http://sourceforge.net/projects/kpedit/

Makeagif (online) - http://www.makeagif.com/
Mask (compare & mark similar pixels) - http://remcodek.home.xs4all.nl/down_tools.html
Microsoft Gif Animator - https://archive.org/download/MicrosoftGifAnimator
MOV2GIF - http://www.softpedia.com/get/Multimedia/Graphic/Image-Convertors/Cyber-D-s-MOV2GIF.shtml
Moving Sketch - http://www-ui.is.s.u-tokyo.ac.jp/~takeo/research/rigid/movingsketch/index.html
 (research prototype distributed for demonstration purposes)

OpenToonz - https://opentoonz.github.io/e/index.html

Pencil 2D - http://www.pencil2d.org/
Picasion (online) - http://picasion.com/
Pivot Animator - http://pivotanimator.net/
PixFlip Animator - http://hansentech.com/pixflip.html

QGifer (save extract) - http://sourceforge.net/projects/qgifer/

Sanologic - see GR44
Scratch - http://scratch.mit.edu
Simple Animator - http://www.codeplex.com/simpleanimator
Skeleton (hpnf) - http://www.freewarefiles.com/Skeleton-V_program_22273.html
SmartMorph - now Popim's Animator
Sprite Vortex - http://spritevortex.codeplex.com/releases/view/60195
Stickman (2d - nffhp) - http://www.easyfreeware.com/stickman_learning_edition-12674-freeware.html
Stykz - http://www.stykz.net/Home.html
Synfig Studio (Gtkmm files req) - http://www.synfig.org/cms/

Tales Animator - http://www.webcartoonmaker.com/ta/index.php
 - http://www.freeware-guide.com/dir/mmedia/animation/TalesAnimator.html
Tapptoons Animation Linetester - http://myweb.tiscali.co.uk/tapptoons/index.htm
Tapptoons Animation Studio - http://myweb.tiscali.co.uk/tapptoons/animationstudiopage.htm
TexRd (animated random textures) - http://www.texrd.com/
TrueSpace - bought by MS & discontinued

Ulead Gif Animator (LFV) - http://www.321download.com/LastFreeware/page24.html
UnFreez - http://www.whitsoftdev.com/unfreez/

Web Cartoon Maker (Andrey Masleyev) - http://www.webcartoonmaker.com/
Winds3D (hpnf) - http://www.brothersoft.com/winds-3d-69592.html
Winmorph - www.debugmode.com

Xtex (seemless Tile browser) - http://www.cybia.co.uk/xtex.htm
WinPlot (draw/animate curves) - http://math.exeter.edu/rparris/winplot.html

----------------------------
online
Gickr - http://gickr.com/
Gifworks - discontinued
Online Image Editor - http://www.online-image-editor.com/
Picasion - http://picasion.com/
Web Cartoon Maker - http://www.webcartoonmaker.com/

List of free animation sites - http://www.dmoz.org/Computers/Graphics/Web/Free/Animated_GIFs/

----------------------------
3d/Stop Motion

3D Base - http://www.yanpage.narod.ru/yan_prg.htm
  (modelling/animation ,Page in Russian, Prog in Russian & English)
Anim8or - http://www.anim8or.com/
Animator HD (was Animator DV Simple - s/n ADV00843072-243) - http://animatordv.com/
Antics 3D Base Pack (hpnf) - 
http://antics3d.blogspot.com/
ClayAnimator - http://www.clayanimator.com/english/clay_animation_software.html
Cyberdelia - http://vixar.jp/cyberdelia/english.html
Helium Frog - http://www.heliumfrog.net63.net/index.html
Jlipsync - http://sourceforge.net/projects/jlipsync/
MonkeyJam - http://www.giantscreamingrobotmonkeys.com/monkeyjam/about.html
Papagayo (lipsync) - http://lostmarble.com/papagayo-home/
SAM Animation (now Hue Animation) - comercial
Stop Mojo - http://www.mondobeyondo.com/projects/stopmojo/
Stop Motion Animator - http://www.clayanimator.com/english/stop_motion_animator.html
WavTracker (lipsync) - http://www.stopmotionworks.com/articles/WavTracker1.0.htm

Info - http://www.stopmotionworks.com/stopmosoftwr.htm