These are some of the applications I use on Mac OS X.

1Password: [App Store]
https://1password.com
Adium:
http://adium.im/
Adobe Lighroom:
http://www.adobe.com/products/photoshop-lightroom.html
BombSquad: [App Store]
http://www.positivespinmedia.com/shareware/BombSquad/index.html
Caffeine: [App Store]
http://lightheadsw.com/caffeine/
Carbon Copy Cloner:
http://bombich.com
CD Text to CD Info Applescript for iTunes:
http://dougscripts.com/itunes/scripts/ss.php?sp=cdtexttocdinfo
Default Apps:
http://www.rubicode.com/Software/RCDefaultApp/
Disk Inventory X:
http://www.derlien.com/
Dropbox:
https://www.dropbox.com
DynDNS Updater:
https://dyn.com/updater-mac/
An assortment of 80's and 90's game console emulators
Enigmo: [App Store]
http://www.pangeasoft.net/enigmo/
EyeTV:
https://www.geniatech.eu/eyetv/support/eyetv-3-en/
ETVComskip (for EyeTV):
https://github.com/essandess/etv-comskip
Firefox:
http://www.mozilla.com/en-US/firefox/
Firewire Video Capture Tools from Apple Firewire SDK (AVCBrowser and AVCVideoCap):
http://developer.apple.com/sdk/#FireWireX
http://connect.apple.com/cgi-bin/WebObjects/MemberSite.woa/wa/downloads
http://connect.apple.com/cgi-bin/WebObjects/MemberSite.woa/wo/5.1.17.2.1.3.3.1.0.1.1.0.3.5.3.3.1
Flame:
http://husk.org/apps/flame/
Flowdock:
https://www.flowdock.com
HandBreak:
http://handbrake.fr/
Homebrew (nginx, certbot):
http://brew.sh
iLok License Manager:
https://www.ilok.com
IntelliJ:
http://www.jetbrains.com/idea/
iStumbler:
http://istumbler.net/
iWork: [App Store]
https://www.apple.com/iwork/
Klondike Forever: [App Store]
http://www.solitaireforever.com/klondike/index.html
Logic Pro X: [App Store]
http://www.apple.com/logic-pro/
Mactracker: [App Store]
http://mactracker.ca/
Make RAM Disk:
http://boredzo.org/make-ram-disk/
Maschine 2
http://www.native-instruments.com/en/products/maschine/
MenuMeters:
http://www.ragingmenace.com/software/menumeters/index.html
http://member.ipmu.jp/yuji.tachikawa/MenuMetersElCapitan/
MetaZ:
http://griff.github.io/metaz/
MPEG Streamclip:
http://www.squared5.com/
Paintbrush:
http://paintbrush.sourceforge.net/
Paw: [App Store]
https://paw.cloud
Bias Peak Express 6:
http://www.bias-inc.com/products/peakExpress6/
http://bias-inc.com/downloads/updates/
QuickTime 7:
http://support.apple.com/kb/DL923
QuickTime MPEG-2 Playback Component (Codec):
http://store.apple.com/us/product/D2187Z/A
Sequel Pro:
http://www.sequelpro.com/
Shrook: [App Store]
http://www.utsire.com/shrook/
Skype:
https://www.skype.com/en/get-skype/
Slack: [App Store]
https://slack.com
SoftEther VPN Server:
https://www.softether.org
SQLite Browser:
http://sqlitebrowser.org
SSHFS (via Homebrew):
https://code.google.com/archive/p/macfuse/wikis/MACFUSE_FS_SSHFS.wiki
Stuffit Expander: [App Store]
http://my.smithmicro.com/stuffit-expander-mac.html
Sublime Text 2:
http://www.sublimetext.com
TextWrangler: [App Store]
http://www.barebones.com/products/textwrangler/
Roxio Toast:
http://www.roxio.com/enu/products/toast/titanium/
VLC:
http://www.videolan.org/vlc/
VMWare Fusion:
http://www.vmware.com/products/fusion/
WebKit:
https://webkit.org/downloads/
Xbox HID Driver:
http://xhd.sourceforge.net/
http://sourceforge.net/projects/xhd/
http://xhd.cvs.sourceforge.net/viewvc/xhd/xhd/Release/
http://macman860.wordpress.com/2013/05/03/xbox-driver-for-mac-os-x-lion/
Xcode: [App Store]
https://developer.apple.com/xcode/