UK:
Scotrail
LNER
Northern (pre-Arriva but I've not been back to Northernland since so I'll include them)
Southeastern
Southern
South West Railway (inc. Island Line)
Virgin Trains
Thameslink
TFL Rail
Greater Anglia (only ever to Stratford though which is a little boring)
Eurostar, I guess
If you were to include former operators: then add in the various versions of Scotrail, the companies that ran the ECML, South West Trains, the old Island Line and I *think* British Rail in the last year of their existence before Scotrail was privatised. Probably going to tick off the various London-area TOCs at some point as I explore places. In London if you stay in Oyster area its easy and can be relatively cheap with my travelcard so sometimes I do the nerdy thing of going on weird routes to places just to go on a different line.
Abroad:
Poland: PKP (both intercity Krakow-Warsaw and a 'local' Krakow-Oświęcim train)
Germany: DB (technically a joint train with PKP Warsaw-Berlin but I'll include them: also pretty sure I got some kind of RER type deal to go from the city centre to Schodenfeld) and the S-Bahn is that counts as non-metro
France: Thalys (Brussels-Paris) and SNCF I *think* (Luxembourg-Strasbourg; I was very tired and travelling for work so wasn't paying much attention)
Belgium: SNCB (all sorts of things; the longest was Brussels-Luxembourg though).
Didn't get a chance to explore the railways in Lithuania a lot which was a shame; especially with the whole different gague thing. Its something that I want to do more of when I travel but, like, I need an excuse for it and that's difficult.