The best two are SoC and CoP, CS is comparatively weak, and rather broken.
Chronologically they go:
CS->SoC->CoP
Though it's better to play SoC before CS (unless you decide to give CS a pass).
All STALKERS barring CoP absolutely require patching.
SoC benefits from ZRP mod, but it's not strictly necessary, CS pretty much necessitates modding, CoP works well enough without mods, but given online activation, crack is recommended.
Their relative strength and weaknesses are as follow:
SoC:
+arguably coolest and most diverse artefacts
+underground labs (where numerous bricks are shat)
+least psychotic animals
+numerous dispersed anomalies
+survival aspect (since there is no repair)
+preciousness of good loot (unique armour, weapons and rare artefacts)
+stealth potential (damn hard, but possible and thus satisfactory)
+arguably most atmospheric
+coolest NV of them all
+best grenades
+best GL and SPAS aiming
+multiple endings, two of which require specific optional tasks to be completed and depend on in-game decision, the remaining ones are essentially game overs, but depend on in-game behaviour.
+cool music in the radios in camps, meshes well with the atmosphere
+firing RPG-7 is just
+nice mystery buildup for the majority of the MQ
+least resource demanding
-no repair or upgrade mechanics
-anomalies are fairly conspicuous
-AI doesn't throw grenades and often dies stupidly to environmental hazards (ZRP helps)
-artifact hunting is often trivial and doesn't involve dedicated mechanics
-broken economy
-fairly bright nights
-some enforced linearity
-endgame is fairly heavy on combat and light on the atmosphere
-no anomaly fields with additional environmental hazard
-stash mechanics doesn't reward exploration (this doesn't mean that the entire game doesn't reward exploration as many cool things can be found, only that there is no point searching for unmarked stashes)
-no free play (ZRP can fix that)
-true endings are what due to the final revelation which is what.
-shit sidequests with shit writing
-Sid's door bug (fortunately you can fix it with in-game means)
-fairly buggy
-least visually impressive
CS:
+the most lethal anomalies in the series, challenging anomaly fields with environmental hazards
+upgrade and repair mechanics
+new areas - swamp and especially Red Forest (the latter will make you shit bricks)
+more paths between areas
+spatial anomalies
+guides as a form of paid fast travel
+extensive faction mechanics
+in soviet Ukraine AI popamoles YOU
+arguably the best economy
+improved terminal ballistics (penetration and stuff)
+makes actual use of DX10 if you have it (only noticeable when it rains).
+dark nights
G
+emissions
+that one cave in RF
+Cordon MG sequence
-that one cave in RF
-Cordon MG sequence
-broken in flight ballistics
-most action-centric
-no NPC incapacitation
-invulnerable bloodsuckers
-nerfed grenades
-AI being able to hit you with several of those nerfed grenades directly from half a map away even if you're sitting on a tree top
-broken NV
-broken pistol aiming
-broken GL aiming (with the exception of FN2000 and RG6)
-broken SPAS aiming
-no interesting 'dungeons'
-being able to break your game in one spot by exploring too much
-upgrade mechanics offering little freedom
-endgame clearly made by one person pulling an all-nighter with a laptop and a bottle of vodka, seriously, it's disjointed, linear and alpha version/poor mod bad.
-stash mechanics doesn't reward exploration
-broken AI behaviour making achieving some objectives frustrating
-auto-holster mechanics in camps making achieving some objectives frustrating when broken AI behaviour forces you to go solo
-CTD causing bugs and conditions necessitating reload of often a much earlier save
-buggy, often gamebreakingly
-no requirement to eat
-no unique weapons
-protagonist has a face you'd instinctively shoot
CoP:
+ealborate diverse anomaly fields, often pretty breath taking
+good quests with a lot of nonlinearity and C&C
+least focus on combat, especially with NPCs
+situational perks masquerading as achievements
+polish and attention to detail (Marked by Zone achievement and soundtrack, for example)
+extremely rewarding exploration
+diverse mutant behaviour
+good upgrade mechanics with unrestrictive upgrade trees
+refined and realistic fast travel system using random NPCs and involving cost
+ability to sleep
+separate helmets
+the best artifact hunting (but see the minuses)
+unique weapons are back
+incapacitation is back
+new items including weapons, meds, and different scopes
+decent NV
+dark nights
+free play
+Fallout style ending depending on choices you've made and those you didn't
+atmospheric locations and atmosphere of desolation in Pripyat
+you need to eat again
+the best writing in the series
+emissions
+medics
+the best NPC interaction in the series
+fairly non-buggy
+makes actual use of DX10 if you have it (again, you will only notice it during the rain)
-least lethal anomalies and hazards
-almost complete lack of dispersed anomalies
-stealthy missions with stealth scripted to fail at some point
-GL (with the exception of FN2000 and RG6) and SPAS aiming still broken
-grenades still nerfed (but not as much)
-fairly short (discounting free play)
-few dungeons, not particularly scary
-unfinished Pripyat with artifical restrictions
-economy is broken
All:
-mirrored weapon models, .45 desert eagle
-daily sun movement is seriously fuck up man