Linux

• LibreWolf as my browser (it's a more secure and private version of Firefox, comes with a pre-installed adblocker and removes all the unnecessary junk) (Flatpak) with some of the following extensions:
  • LibRedirect for redirecting privacy-invasive websites to private frontends
  • ff2mpv
  • Read Aloud (text-to-speech)
  • Buster for solving CAPTCHAs
  • Dark Reader
  • Violentmonkey for userscripts like Lemmy Universal Link Switcher (it's really useful)
  • DownThemAll
  • Search by Image
  • Server-Status (GitHub) shows information about a web server like country/region (via local GeoIP database lookup), SSL certificate information and more. Good open source alternative to Flagfox.
• Thunderbird for emails (Flatpak)
• Proton Mail Bridge (Flatpak)
• Merkuro Calendar
• Ptyxis (Flatpak) as my terminal. It's optimized for containers (e.g. distrobox). foot is a pretty good alternative if you want something more minimalistic and don't care about containers. There are countless other good options like Kitty, Alacritty, Konsole, WezTerm and many others.
• Emacs as my IDE
• KWrite, Kate or NotepadQQ for quickly editing text documents. There's also Apostrophe for GNOME.
• QOwnNotes for local/Nextcloud-synced notes (Iotas for GNOME) There are other good options like Trilium Notes or Joplin.
• Speech Note speech-to-text note-taking (https://piped.video/watch?v=zlLVgTB42Bo)
• Akregator as my RSS client (Newsflash for GNOME)
• Strawberry as my music player (Amberol or Rhythmbox if you're on GNOME)
• Spot for Spotify (Flatpak)
• Cider for Apple Music (unfortunately not FOSS anymore)
• Feishin for connecting to my self-hosted Navidrome music server
• rescrobbled for saving my music listening history to Last.fm. Also works with self-hosted ListenBrainz.
• Jellyfin Desktop for connecting to my self-hosted Jellyfin media server
• mpv as my video player (Celluloid on GNOME)
• FreeTube for watching YouTube videos
• This modded YouTube Music client that has an adblocker and many other cool features: https://th-ch.github.io/youtube-music/
• Kasts for listening to podcasts (also has the ability to sync with gpodder.net or self-hosted GPodder on Nextcloud)
• LibreOffice (Flatpak) There's also OnlyOffice.
• Skanpage for scanning documents
• GNUcash for accounting
• Notesnook or Standard Notes for end-to-end encrypted note-taking
• Anki Flashcards (Flatpak)
• Logseq (FOSS Obsidian alternative)
• Flameshot for screenshots (GitHub, Flatpak)
• Kdenlive for video editing
• GIMP, Krita and Inkscape for graphics stuff
• Blender for animation stuff
• Natron for VFX
• LMMS and Ardour for music production
• Virtual Machine Manager for creating/managing KVM/QEMU VMs (Boxes for GNOME)
• Nextcloud Desktop for connecting to my home server
• Signal Desktop (Flatpak) There's also Flare for GNOME, which uses GTK instead of Electron and feels more native (Flatpak)
• Element (or NeoChat if you use KDE, Fractal for GNOME) for Matrix
• WebCord for Discord. There are some native GTK clients like Abaddon and Dissent.
• Paper Planes (Native GTK Telegram client)
• Konversation or HexChat for IRC (Polari on GNOME)
• Tokodon as my Mastodon client
• qBittorrent for downloading torrent content. (You can use KTorrent on KDE and Fragments on GNOME)
• Pika Backup for taking backups (There's a pretty good video about it: https://piped.video/watch?v=W30wzKVwCHo)
• Timeshift for btrfs snapshots
• Gradience to customize GTK4 appearance
• Bitwarden for syncing my password database with my self-hosted Vaultwarden server (also works with their public cloud syncing option). Use KeePassXC if you prefer something entirely local.
• LocalSend for sharing files on the local network (basically works like AirDrop) (also works over NetBird or Tailscale btw)
• NetBird for creating a flat VPN network between my devices
• KDE Connect for better integration with my phone. Also works over NetBird btw. Check out GSConnect if you're on GNOME.
• KRunner for quickly finding files or applications (Ulauncher for other desktops, rofi for window managers)
• Safing Portmaster (Firewall and DNS blocking solution. Check out OpenSnitch if you just need a firewall)
• LACT for controlling AMD GPUs
• Flatseal for managing Flatpak permissions (On KDE this is integrated in the system settings)
• Bottles for managing Wine prefixes (Flatpak)

If you like gaming:

• Lutris for managing my games
• Heroic for Epic Games and GOG
• Prism Launcher for Minecraft
• Dolphin for emulating Wii and GameCube
• Ryujinx for emulating the Switch
• RPCS3 for PS3 emulation
• Vita3K for PSVita emulation
• PPSSPP for PSP
• Cemu for Wii U emulation

For the CLI:

• fish shell
• starship
• tmux
• fd as an alternative to find
• bat instead of less (written in Rust, has some nice syntax highlighting)
• ripgrep
• fzf
• zoxide
• yt-dlp
• streamlink
• ncmpcpp
• ncspot
• newsboat

Logseq.

I don't know about you specifically, but I'm surprised how many people haven't heard of Krita, a FOSS image editing app with an optional AI Image Generation plugin.

The first things I install on a fresh linux install are always htop (task manager) and micro (nano but better).

edir to mass-rename

fd is more convenient than find

aria2 makes downloads go brr with parameters -x 10 -k 5M and is integrated with multiple tools like yt-tlp, yay

Oh, and pass for password-management

ssu makes root console tools password-less. That and rdo for gui-tools (both a bit over 100 loc) made me uninstall sudo.

EDIT: realized this was for desktop, so removed the original list of mostly android apps. Here's my go to desktop apps:

Lollypop - music player
Invoiceninja - open source invoicing service
Meld - file/folder comparison
Librewolf - hardened Firefox
Joplin - notes
QEMU/Virt-Manager - virtualization for that one windows app you still need
KeepassXC - password management
Element-desktop - Matrix client
Gparted - no fuss partition management
Lutris - game launcher that works with epic games (among many others)
PDFarranger - best PDF management I've found on Linux Soundconverter - easy to use file converter
Restic - backups
Fdupes - duplicate file finder
Freetube - privacy respecting YouTube client
Paperless-ngx - very well built electronic document storage. Must be run as a server.

Emacs.

Emacs is an app platform in and of itself, and the vanilla installation comes with dozens of its own apps pre-installed. Like how web apps are all programmed in JavaScript, Emacs apps are all programmed in Lisp. All Emacs apps are scriptable and composable in Lisp. Unlike on the web, Emacs encourages you to script your apps to automate things yourself.

Emacs apps are all text based, so they all work equally well in both the GUI and the terminal.

Emacs comes with the following apps pre-installed:

• a text editor for both prose and computer code
• note taking and organizer called Org-mode (sort of like Obsidian, or Logseq)
• a file browser and batch file renamer called Dired
• a CLI console and terminal emulator
• a terminal multiplexer (sort-of like "Tmux")
• a process manager (sort-of like "Htop")
• a simple HTML-only web browser
• man-page and info page browser
• a wrapper around the Grep and Find CLI tools
• a wrapper around SSH called "Tramp"
• e-mail client
• IRC client
• revion control system, including a Git porcelain called "Magit"
• a "diff" tool
• ASCII art drawing program
• keystroke recorder and playback

Some apps that I install into Emacs include:

• "Mastodon.el" Mastodon client
• "Elfeed" RSS feed reader
• "consult" app launcher (sort-of like "Dmenu")

Because you asked about "apps", people are replying with mobile apps. I think you wanted to write "programs" considering the community. Maybe you should edit this

Thrown away your current ssh client and get

https://xpipe.io/

NewPipe

Someone already mentioned Logseq, but I'm really enjoying Obsidian for my note taking needs. It's similar, but I have found Obsidian to be very nice. Not FOSS, but I really like what the devs are doing.

KDE Itinerary. To keep all your travel (rail tickets, hotel reservations...) documents and Infos in one place.

Tokodon/Tuba a great mastodon client for KDE and GNOME respectively

Lollypop a beautiful and useful Mediaplayer and Jukebox for GNOME.

Geary a great mail client by the same developer as Lollypop, also for GNOME.

Not necessarily unheard of but Floorp has been pretty great for work. I think all of the other applications I use are well known within their respective niche (e.g JOSM)

A lot of good stuff here. The three things that are most notable for me are:

Notepadqq

Fsearch

Librewolf