What are your favorite privacy programs you use frequently?

Matrix messaging apps. It's nice to have modern messaging features, end-to-end encrypted, with no single point of failure, no Google involvement, and no phone numbers. I expect to start recommending it widely when the 2.0 features land in the popular clients.
WireGuard VPN. It's fast, even on low-power devices.
Self-hosted Mumble. Excellent low-latency voice quality for chatting or gaming with friends.
Radicale, DAVx⁵, and Thunderbird, for calendar and contact sync between mobile and desktop, without handing the data over to Google or anyone else.

Lots.
However I want to give FreeTube some love. Out of all the YT frontends, FreeTube has never failed me and always been a treat to use. I've used it on both Linux and Windows, and the experience is always reliable.
- Freetube who is the Dev? I find several apps named this.
  
  https://github.com/FreeTubeApp/FreeTube
- By far my all-time favorite app - Freetube. Used to be KDE Connect for transferring files between devices, and still is an useful app. But man Freetube is amazing

For me the fediverse and Librewolf on Linux
- I'm the same here as I too use the Fediverse and LibreWolf, but we shouldn't kid ourselves about the former: by the very nature of how the Fediverse works, it is honestly pretty damn terrible for the purposes of privacy. Unless I'm missing something, which mind you is certainly a possibility.
  
  i mean it's in the name:
  FEDiverse
  
  I think the fediverse does have a privacy problem, however as long as your account can’t be linked to you (malicious instance, your email being breached) it doesn’t matter all that much (at least for my threat level) because the info is confined to the fediverse, where little can be done with it, especially if you swap instances/accounts commonly. Yes, one could create a profile on you based on what you upvote/downvote, but they can’t for example use that to serve targeted ads, because the fediverse doesn’t have a ad network and when visiting other sites they can’t associate your profile with you (assuming you don’t reuse your username), unless I am forgetting something.
  tldr: The fediverse isn’t private, but the data is practically useless
- Ones like Lemmy fit in fine to my threat model. They enable me to use privacy tools up-to-and-including Tor routing, without a phone number or other personally identifying info (you can't do those with many other social media platforms). I can use the Fediverse pseudonymously, and if I ever want to, anonymously.
  I'm not hiding this conversation from you, but I am hiding my identity from companies.
  
  obviously public fora content is not meant to be private but using a fedi instance is privacy focused solution vis-a-vis redidt who tracks ever fucking click and finger prints your browsers while permittitng rando creeps like sundar and faceberg to do the same.

MullvadVPN, and a free and privacy respecting OS is another good idea.
So is using privacy respecting apps: LibreOffice instead of MS Office, Codium instead of VSCode. And so on, with many FLOSS alternatives to the usual proprietary ones.
Services also matter, imho: I'm using ProtonMail for my email (Tuta would be another clever choice, imho, and there are probably others). I've very recently switched from iCloud to filen.io for my cloud storage needs.
Using one's phone as little as possible. I've almost nothing on mine, I mean only stuff I'm required to have (banking and IDs, stuff like that), no email, no social, not even music or games (the game I enjoy the most play I also I enjoy it the most when I play it offline: chess ;))
And then... I also started using analog tools much more in the last two years. This helps a lot maintaining one's privacy. Amazon can't track my reading habits when I read a printed book (even less if I do not buy it from them), Goofle cant'" track my writings when I use pen and paper instead of their apps, Apple (or Google or Microsoft) can't track my paper agenda or my paper notebook. And the NSA or whomever is playing that role in my country can't ask any corporation to install backdoors in my IRL encounters with people so they could spy on me. At least, they cannot do that for now ;)

Monero, SimpleX

Openwrt on my flint 2 With adgaurd/pihole I know its not technically an app, but lots of people forget there routers exist and are a very big security hole
You would not believe what my samsung tv pings
Tiktok (somehow came preinstalled)
Hulu(we dont have a hulu account)
Tubi(we dont use tubi)
Amazon(it seems to be for samsung tv plus)
I ended up blocking everything except amazon, samsung tv, and netflix on the dns level
Its also really good for stopping non power users (aka family member's) from getting malware/phished
--edit fixed formatting

ProtonVPN – VPN
LibreWolf – Browser
uBlock Origin
Skip Redirect
NoScript
Decentraleyes
CookieAutoDelete
DuckDuckGo Privacy Essentials (tbh I'm not sure if this isn't redundant frankly what with the others I have installed; might get rid of it...)
KeePassXC – Passwords
FreeTube – YouTube

I don't do much. Just changed dns to next dns, and set firefox to whipe all on exit.

XMPP + OMEMO & Mumble for chat, offline maps from OSM, self-hosted feed aggregator
NixOS, OpenWRT, LineageOS for microG, but would like to remove Android from my line up.
- What would you replace Android with?
  
  Linux, Capyloon, KaiOS… kinda don’t care so long as it isn’t controlled by some US megacorporation

I made my own list of software, and most of those listed are software I use daily.

Tubular (NewPipe + Sponsorblock), Fedora, Mastodon through Tusky, Lemmy through Eternity. Still waiting for LineageOS image for my phone (SM-A536B) tho.

Instead of naming my all time favorites I'll name my most recent favorites...
Inter Profile Sharing - FOSS app to share files and text between android profiles. Super useful as a GOS user.
WG-tunnel - A way more feature rich version of the Wireguard app.
- I needed inter profile sharing so so so many times. No more texting myself photos! Damn I can't believe I didn't think of this.
  
  Author says it should work even in airplane mode which is pretty cool.

Freetube instead of youtube,
Thunderbird calendar instead of something like google calendar,
Signal instead of Discord or text,
Tellico for all media lists instead of something like goodreads or online movie or game lists,
Obsidian or Joplin for notes and organizing creative pursuits
- Which free tube app there is several? I was using libretube or something but it bugs out a lot.
  
  https://github.com/FreeTubeApp/FreeTube
  Not available through the Google Store. The APK is on their Github page - https://github.com/FreeTubeApp/FreeTube

Fossify mobile suite: It contains all basic tools from a launcher to a notes app
Clipious: Open source youtube frontend
Obtainium: Frontend to download apps
FluffyChat: Matrix client
Vanadium: Secure chromium fork
Mull: Less secure then Vanadium but Firefox based
Thunderbird: Lemmy client
Termux: Android terminal
Thunderbird: Open source email client (now on mobile)
HeliBoard: Open source keyboard

Rethink DNS.
I'm running stock android for work reasons, Rethink is awesome

CommonSense 2024, the best antivirus solution I’ve ever tried. Highly recommend it. Compatible with phones, tablets, computers, potatoes etc.
- But is it compatable with my 1999 toaster. It can run doom if that helps
  
  If it supports Electricity V 230, you should be fine. If it’s still on V 120, all bets are off.

Some outside what others may say. Depends on what you're trying to make private.
Self-hosted Vaultwarden/BitWarden, SearXNG, and Firefox Sync. All things missing from your list to privatize the web.
Signal/Matrix for chat.
Organic Maps when you don't need traffic for privatizing location.
Self-hosted Nextcloud for file storage.
And Obtainium (and gam for Linux) to break away from the stores themselves.

I use open-source applications that don't require internet access for tasks that can be done perfectly offline, which is great not just for privacy but for many other reasons as well.

Cromite.
- Mulch is a mobile chromium browser made by DivestOS (same folks who make Mull). Maybe worth checking out over Cromite.
  
  Why?
  Cromite is excellent.
  Too bad it's chromium based, but works a whole lot smoother and snappier than Firefox based browsers, oh and safer as well.... So for the time being, Cromite it is.
  Librewolf on desktop Linux is my weapon of choise.

Honestly, just Unbound for DNS filtering + Tailscale + commercial VPN solves 99% of my problems with privacy online.
- Tailscale
  Have you considered Headscale?
  
  I really wanted it to work on Fly.io but I couldn’t get it to. I’d also like to get the Tailscale software Dockerized but running multiple nodes on the same host with custom DNS was a complete shitshow.
  I really love Tailscale, but the daemon and CLI seem to be absolute garbage.

- What is i2p good for? I install it evert now and then, give it a whirl, and then uninstall it

Favourite: GrapheneOS
Others that I like: Monero Librewolf SimpleLogin MullvadVPN PiHole

Right now it's whipper, beet, Navidrome and Symphonium.
I'm buying cheap CDs in thrift stores and ripping them and really enjoy listening to my own music on my own devices.

Pi-Hole for home Wifi, Guest Wifi for IoT devices. For Desktop PC I use Linux, hardened Firefox, uBlock Origin extension. For the Phone I use NextDNS, work Profile for IoT apps, and F-Droid for some apps.

It's not about what you use, it's what you don't.

Invizible pro, Cromite, Apktool M/MT Manager (for manually reverse engineering apps), App Manager (for finding spywares in apps), Warden (for disabling them)