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.
Audile: offline, trackerless music recognition.
Keepassdx + Heliboard: both excellent apps in their own right that create a smoother experience of mundane phone use, but they also integrate rather well together and Heliboard will often pop Keepassdx in to its suggestion bar when you enter a log in page. It's been really nice for me.
FUTO voice input: speech to text for those who don't want to use Google speech services. Frankly, the FUTO app works better than googles app anyways, it always handles grammar correctly as long as you speak relatively clearly, and integrates with Heliboard nicely.
Tailscale: for those who need VPN access to their other devices.
Thunder : a Lemmy client with compatibility with Lemmy's recent server side changes and also has a decent UI/UX
tasks.org: fantastic, customizable to do app with various syncing options.
Magic Earth: privacy respecting maps/directions for those who don't want google maps. (NOTE: closed source. Here is the privacy policy, terms of use and description of their business model at the bottom of their FAQ)
Myne: e-book downloader.
Markdownr: convert webpages to markdown. Great option for mobile, if I'm on desktop I use the Joplin web clipper plug in for Firefox.
Seconding Newpipe, excellent app.
EDIT: added links to the terms, policies and FAQ of Magic Earth, as it is not open source.