Video Game Series With Complex Timelines

To be updated with more examples as I can think of them.
Dates are Anno Domini/Common Era unless otherwise noted.

THE LEGEND OF ZELDA 
Skyward Sword
The Minish Cap
Four Swords
Ocarina of Time - Split into three timelines after this (A, B, C)
B) Majora's Mask
A) A Link to the Past, B) Twilight Princess, C) The Wind Waker
A) Oracle of Ages & Oracle of Seasons, C) Phantom Hourglass
A) Link's Awakening
A) A Link Between Worlds, B) Four Swords Adventures, C) Spirit Tracks
A) The Legend of Zelda
A) The Adventure of Link

METROID
2075 CC (Cosmic Calendar) - Metroid/Metroid: Zero Mission
2076 - Metroid Prime
2076 - Metroid Prime: Hunters
2077 - Metroid Prime 2: Echoes
2078 - Metroid Prime 3: Corruption
2079 - Metroid II: The Return of Samus
2079 - Super Metroid
2080 - Metroid: Other M
2081 - Metroid: Fusion
 
CASTLEVANIA
1094 - Castlevania: Lament of Innocence
1450 - Castlevania Legends
1476 - Castlevania III: Dracula's Curse
1479 - Castlevania: Curse of Darkness
1576 - Castlevania: The Adventure
1591 - Castlevania II: Belmont's Revenge
1691 - Castlevania/Vampire Killer/Haunted Castle/Super Castlevania IV/Castlevania Chronicles
1698 - Castlevania II: Simon's Quest
1748 - Castlevania: Harmony of Dissonance
1792 - Castlevania: Rondo of Blood/Castlevania: Dracula X/Castlevania: The Dracula X Chronicles
1797 - Castlevania: Symphony of the Night
180X - Castlevania: Order of Ecclesia
1830 - Castlevania: Circle of the Moon
1844 - Castlevania: Legacy of Darkness
1852 - Castlevania 64
1897 - Bram Stoker's Dracula
1917 - Castlevania: Bloodlines
1944 - Castlevania: Portrait of Ruin
2035 - Castlevania: Aria of Sorrow
2036 - Castlevania: Dawn of Sorrow
-- The (POS) "Lords of Shadow" games take place in a new, rebooted continuity--
1047 - Castlevania: Lords of Shadow
1073-1103 - Castlevania: Lords of Shadow - Mirror of Fate
2057 - Castlevania: Lords of Shadow 2

METAL GEAR
1964 - Metal Gear Solid 3: Snake Eater/Metal Gear Solid 3: Subsistence
1970 - Metal Gear Solid: Portable Ops
1974 - Metal Gear Solid: Peace Walker
1975 - Metal Gear Solid V: Ground Zeroes
1984 - Metal Gear Solic V: The Phantom Pain
1995 - Metal Gear
1998 - Snake's Revenge
1999 - Metal Gear 2: Solid Snake
2002 - Metal Gear: Ghost Babel
2005 - Metal Gear Solid/Metal Gear Solid: Integral/Metal Gear Solid: The Twin Snakes
2009 - Metal Gear Solid 2: Sons of Liberty/Metal Gear Solid 2: Substance
2014 - Metal Gear Solid 4: Guns of the Patriots
2016 - Metal Gear Acid
2017 - Metal Gear Acid 2
2018 - Metal Gear Rising: Revengeance

ASSASSIN'S CREED
The framing story of Desmond Miles takes place entirely between September and December 2012.
1190 - Assassin's Creed: Altair's Chronicles
1191 - Assassin's Creed
1192 - Assassin's Creed: Bloodlines
1476-1499 - Assassin's Creed II
1499-1507 - Assassin's Creed: Brotherhood
1511-1512 (1190-1257) - Assassin's Creed: Revelations
1712-1725 - Assassin's Creed IV: Black Flag
1753-1783 - Assassin's Creed III
1765-1777 - Assassin's Creed: Liberation