Just installed Sierra and wanted to see what works. So far from my testing the below work for me.
MOD EDIT: This is a wiki post, which is editable by anyone with the appropriate rights. Please update this post with compatible and incompatible apps to ensure the list is comprehensive. For apps with limited compatibility, please include a link to your post explaining the limitations. The lists are in alphabetical order.
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Compatible
1Password 6
2Do
Accordance Bible
Adapter
Adium (requires manual connection)
Adobe Acrobat Pro 10 (Not my experience with Acrobat Pro 11.0.16 - See Below)
Adobe Acrobat DC
Adobe Photoshop CC
Affinty Photo
Airmail 3
Alfred 3
Amphetamine
AppZapper
Atom 1.7.4
BackBlaze 4.0.5.934
Banktivity 5 (formerly iBank)
Better Rename 9
BetterTouchTool
BetterSnapTool
BitTorrent Sync
Blackmagic Disk Speed Test
Caffeine
CARROT Weather
Chatology
Checkbook Pro
Chrome 51.0.2704.84
Cloudmagic
coconutBattery
Coda
Continuity Activation Tool
DaisyDisk
Dark Boot 4.0.6
Day One v2
Deliveries 2.0.1
Discord
Disk Inventory X
Disk Warrior 5.0
Downie 2.3.9
Drobo Dashboard
Dropbox
Duet (with iOS 10, although a bit choppy)
Evernote
Fan
Fantastical 2
Fetch 5.7.5
Final Cut Pro X (launches but have not used)
FileZilla
Firefox
Flux
Font Book (fixed in second beta)
Google Drive Desktop App
Handbrake
HardwareGrowler
Hardware Monitor
HoudahSpot 4.2.1
iDrive 3.4.0.15
iFlicks 2
iSkySoft iTube Studio 5.7.1
iStat Menu 5.11
iStat Pro
Itsycal
Kodi
LastPass
Letterspace v1.6.4
Little Snitch Nightly build 3.7 (
https://www.obdev.at/products/littlesnitch/download.html)
LogMeIn
Magnet
Malwarebytes
Microsoft Office 2011 (All Applications)
Microsoft Office 2016
Mindnode
Minecraft 1.10
Moom
Mountain
MPlayer OSX Extended
MySQL Workbench 6.3.6
OmniFocus 2.5.3
OmniGraffle 6.0.4 (quite old)
OmniGraffle 5.4.4 (even older)
OpenEmu
Opera
Outside 1.1.3
ownCloud Client 2.2.0
PaintCode 2.4.2
Parallels 11.2.0
PDF Expert
Pinegrow Web Editor v2.9
Pixelmator (Magic Wand causes crash every time it is used, other than that no other observed issues)
Plex
Pocket 1.6.2
Polar FlowSync 2.6.4
PopClip
PrintCheck
Pyware versions 8.0.1 and higher (due to using Oracle's Java and not the old MRJ)
Quicken 2007
Quicken 2015
Quicken 2016
QuickSleep 1.0.1
Quiver 3.0.2
Reeder
Scrivener
ScummVM
Shazam
Sketch 3.8.3 by Bohemian Coding
Skitch 2.7.8
Skype 7.30 (274)
Slack 2.0.3
Spotify (although slow to launch and ever the memory hog)
Steam (Code signature error, needs to be manually signed)
StuffIt Expander
Subler
SuperDuper
Telegram (As of 6/20 update is unstable:
https://macos.telegram.org)
Telegram Desktop
Text Expander 5.1.4
The Unarchiver
Transmission
Transmit
TunnelBear
TunnelBlick
Tweetbot 2.4 (though sometimes, tweets appear blank or empty... closing/restarting Tweetbot fixes the issue temporarily.)
Twitter
Vivaldi Web Browser (1.2.490.39) (64-bit)
VLC
Yummy FTP
XLD
Limited Compatibility
Aperture 3.6 (limitations listed in Sierra release notes)
Acrobat Pro 11.0.16 - Will not Print. I can still create and alter documents, but they will not print from the application. The fix is to print from Acrobat Reader DC.
CleanMyMac 3 will prompt to install a beta release that supports Sierra (3.5b2)
Disk Sensei (launches but loses Trim support after restart) Trim Enabler works. Trim force command in Terminal does not!
Fusion 8.1.1 (see
this post)
gfxCardStatus (displays GPU status, but will always force discrete GPU since gfxCardStatus "requires" the discrete GPU)
Hazel (some rules do not work)
Logic Pro 9.1.8 (can crash intermittently)
Simple Comic (will not install latest update but reads CBR files okay)
uTorrent (can crash in certain circumstances)
VM Ware Fusion 8 (Turn of 3D acceleration if you get an "Internal Error")
iBank 4.7.5 Gives an error on exit but added/updated transactions are saved.
Incompatible
Adobe Dreamweaver CS5 (crashes on launch)
Adobe Dreamweaver CS6 (must reinstall Java 6, opens and functions, crashes on Save As...)
Adobe Illustrator CS6 (installer error, if update from prior OS, make work after reinstall Java 6)
Adobe InDesign CC (installs, but has some rendering issues when dragging objects)
Adobe Photoshop CS5 (crashes on close)
Adobe Photoshop CS6 (installer error, make work if update from prior OS)
Bartender 2 (crashes at launch)
BOX Sync (brings up Console, floods with errors, doesn't work at all)
BusyCal (crashes at launch)
Carbon Copy Cloner 4.19 (installs and opens for use but does not actually backup)
CCleaner (does not open)
Citrix Receiver
Contacts (Apple's Application) Crashes FOR SOME at launch
Disk Warrior (launches and works for a while but crashes in the end before replacing the rebuilt directory)
EazyDraw 7 (crashes at launch)
EtreCheck (crashes during scan)
Final Draft 9 (crashes at launch) (Update to 9.0.9 fixes problems)
Fluid (any apps made with Fluid crash on startup)
Freemacsoft LiteIcon 3.6.3 (Error message at launch even when SIP is disabled)
F5 Big-IP Edge Client (VPN) - App opens but will not connect
Greek Radio (icon has slash through it, Sierra throws error when launching)
iBooks (crashes at launch)
Identify 551
Little Snitch 3.6.3 (see nightly build instead
https://www.obdev.at/products/littlesnitch/download.html)
Logitech Control V3.93 Doesn't recognize my Logitech Performance Mouse (Logitech Unifying Software V1.2.315 works). What this means is that my Logitech Mouse is Recognized, but just the left and right buttons work along with the scroll wheel. None of the other buttons can be programmed Because Unifying Software does not recognize the mouse.
Maintenance (crashes at launch)
Microsoft Office 2008 (crashes at launch)
Microsoft Office 2011 (Word, at least, crashes attempting to open a file) - All Microsoft Office 2011 Applications are working fine for me in the Public Beta
Onyx (crashes at launch)
MPlayerX
Pulse Secure 5.2r2 (backend dsAccessService seg faults when run)
Pyware versions 8.0.0, 7, 6, and lower (due to Apple's MRJ Java--not able to be installed on 10.12)
Quicken Essentials for Mac 1.7.4 (icon has slash through it, Sierra throws error when launching)
RapidWeaver 7 (Opens projects and appears to work but crashes when previewing Site)
Razer Synapse 2.0. (Loads but can´t detect device)
Safari Technology Preview 9.1.2
Scansnap Manager (crashes while trying to save the PDF)
SyncTwoFolders 2.19 (Crashes after selecting destination or target folder)
Ulysses (crashes at launch)
Yosemite Disk Utility patched for El Capitan (crashes at launch)
Microsoft OneDrive (Crashes at Launch)
Western Digital Disk Tools (Complains about needing to be launched from Applications folder)
WhatsApp Desktop (always recommends moving to Application folder when it is already there, and will lose login details prompting QR scans every time OS restarts)
WriteRoom 2.5.1 (marked as incompatible)
ZenMate (makes initial VPN connection then disconnects)