Complete MGS timeline:
- MGS3
- MGS
O
- MGS
W
- MGS:GZ
- MG
- MG2: SS
- MGS
- MGS:Mobile
- MGS2: SOS
-In between, Policenauts
- MGS4
MGR:R
- Snatcher
- ZOE
- ZOE2:TSR
All the other Kojima games are related to the Metal gear universe with multiple story and names connections and with many recurring chracters.
PS: I didn't include MGA and MGA2 because I didn't play them and they probably don't fit in like OAVs in anime.