IRC and email are, I’m pretty sure, the only two that are used outside of an ideological niche.
IRC was properly decentralised very early on, but due to spam, attacks, takeovers, etc. it evolved into a handful of seperate, closed, networks (efnet, freenode, etc.). These days it’s been mostly replaced with fully centralised services.
Likewise, email was completely decentralised but over time (and for similar reasons) it has become very centralised to just a few large providers (i.e. Gmail, Outlook, Yahoo, and sending services like Mailgun and MailChimp). And while running your own mail server is still possible it requires frequent upkeep and configuration to ensure all those large providers keep accepting your mail.
I suppose you could also include BitTorrent and DHT as well, they are decentralised and seem to work fairly well, though it can and has been flooded with fake peers and requests in the past.
As far as I know, new decentralised services like Mastodon and Matrix are yet to run into and deal with those problems (I’m happy to be shown otherwise).