KDE's Dolphin + Konsole's integration to Dolphin is great for seamlessly managing files with an UI and terminal hybrid.

Though closed source (overly dramatic music plays), the text editor Sublime Text works great, and at least with major version 3 (last I checked it was in version 4), it can be converted to AppImage without major issues (at worst, paths with spaces have issues).

Firejail is great for starting specific programs offline.

Newsboat is the best RSS feed reader I could find for Linux, specifically due to, with its inbuilt macros, I can set it up to open in new tabs several posts from a comically large amount of feeds.

Ocenaudio for audio editing. It's not FOSS but it's native, simple to use, and doesn't have backend library issues I kept having with audacity.

UpNote. I use it like a combination of the gollum wiki described by OP, but I just put everything in there. I have watch and reading lists for things I want to check out, writing projects, notes for TTRPG games, I keep extensive notes on healthcare-related stuff, and so on. I like UpNote because it's lightweight, has windows, linux, and android apps, and because it has a one-time $25 lifetime membership that does free syncing forever instead of a monthly subscription like most other things seem to. I've tried OneNote, Evernote, Obsidian, Joplin, AnyType, and a bunch of others and didn't like them for various reasons, but UpNote is both pretty small and also has a pretty full-featured editor that can do rich text, all kinds of formatting, media files, etc.

The only thing I've run into that UpNote wasn't ideal for is I started writing a novel a couple months ago and managing the structure and notes and all that got a little unwieldy so I picked up Scrivener. Still wish they had an updated linux client or there was some good, complete, feature-rich linux-native equivalent, but it runs pretty good under wine, so.

I do a fair amount of pentesting and I'm on mobile, so I'll just list software.

Trufflehog & nosey parker (both kinda suck, but there's nothing better)

Subfinder

Nuclei

Credmaster

To name a few.

I would say Rymdport (https://github.com/Jacalz/rymdport). It's a GUI for the magic-wormhole tool (another recommendation in itself). It let's you easily and safely transfer files to another computer.

Great topic. I'm going to have to investigate some of these suggestions later.

Since my first pick, helix, was already mentioned here and i commented on it, I'll add gitui. Git can be very overwhelming for me. Gitui arranges frequently used git commands in a sensible, visual layout and makes it easy for me to understand and interact with git.

Right now https://jeena.github.io/recoder/ which I just released and here is why (copied from the website):

🎬 Why Recoder?

I used to edit family videos in Kdenlive without a problem — it handled footage from all our devices without complaining. But then I switched to DaVinci Resolve, and suddenly nothing worked right. My Sony Alpha 7C, my Galaxy S24, and my wife's iPhone all produced files that Resolve couldn’t handle without transcoding.

😤 Too Much Fuss, Too Many Steps

Every time I wanted to edit, I had to hunt down the right ffmpeg settings and manually run them on each video — a frustrating and repetitive task.

My typical workflow is simple: I create one folder per event on an external HDD and drop in videos from all our cameras. A script renames the files based on the date and time so I can easily sort them. But for Resolve, everything has to be transcoded to DNxHD — which only supports resolutions like 1920×1080 and 1280×720.

🔄 Vertical Videos? Extra Pain

That also meant vertical videos couldn’t work. So now, I rotate them during transcoding to preserve resolution and rotate them back in Resolve during editing.

✨ Enter Recoder

I built Recoder to automate this annoying step — so I could spend more time editing memories and less time fiddling with command-line tools.

I like game emulation and to manage my ROM library, I use Geode-GEM. It is simple but cusomizable app to manage your ROM based on console and emulator you have.

Ed Along with rlwrap it gives me a very fast and powerful workflow.

Rlwrap It wraps around a program and gives it the ability to make use ofthe readline lib.

Screen I use it when I boot without X. Gives a very fast workflow, being able to switch between programs.

Mpv Multimedia powerhouse. Even works (pretty) well without X, with a framebuffer.

Ecasound Cli daw. Have several scripts to make a recording on the fly or to be able to jam.

Man, I have so many apps, but here are a couple that I install first thing on a new install:
Timeshift is possibly at the top of the list.

Then Deja Dup.

Stacer

Strawberry

Open TV