I'm not sure if it should be best games for historical value or games that are best today (because of better UI but not better gameplay)?
I'll try to list the latter but there will be still many old titles who are still great today and still greatly playable.
5 points
Pirates! (1987) - Yep, it's still the better version.
Master of Orion 1 - The first one has the most elegant design but the second one is great as well.
X-Com EU (1994) - What i can say? DUH.
Civilization - Not sure which version, 1, 2 an 4 all have merits so i'll vote the
2nd one.
Master of Magic - Still the best of it's kind
3 points
Secret of Monkey Island (1990) - THE best point & click adventure game.
Star Control 2 - As someone already mentioned - Definitely NOT an rpg and a truly great game (mostly adventure/action if you ask)
Mount & Blade: Warband (2010) - I consider it an action game with lite strategy and rpg elements. Replace with
CK2 if needed.
Sim City 2000 (1993) - Nothing to say, still a great building game
Europa Universalis 4 - The one I find most playable but Crusader Kings is damn close
1 point
Crusader Kings 2 - Three more great games by Paradox.
Europa Universalis 3
Hearts of Iron 2
XCOM (2012) - Because of the Long War mod
Master of Orion 2
King of Dragon Pass - I will always remember the idiot who gave it 1/10 in Secret Service - a potato game magazine
Railroad Tycoon (1990)
Prince of Persia (1989)
Battle Brothers (2015)
Rome: Total War (2004)
Colonization (1994)
Some more games i considered for 1 point but run out of room
Maniac Mansion 2: Day of the Tentacle (1993)
Heroes of Might and Magic 2
GTA: Vice City (2002)
Freespace (1998)
Flashback (1992) 1994 for PC version. I finished it both on Amiga and PC
Some
morons not very monocled gentlemen included Jagged Alliance 2.
At least one of them included it in the very first place of his whole list.