If you fight the frightener with Vesemir, he will give you a red meteorite when talking with him later. Near the end of Chapter I at the bridge, you will face some Salamandra with a mutant dog, and the cutscene that plays will be generally negative about your choice here.
But if you choose to save the lab with Triss, you can loot a sapphire from Savolla's corpse. At the bridge in Chapter I, you will face the Salamandra only, no mutant dog, and the cutscene will be generally positive about your decision here.
If you give the arms to the Scoia'tael, they will use those weapons to kill Coleman in Chapter II. This happens as soon as you go to The Hairy Bear Inn after speaking with the detective. (So if you intend to complete The Rat Quest, go to the inn before speaking with Raymond, which can be a bit tricky to avoid.)
If you do not give the arms to the Scoia'tael, Golan Vivaldi will be sent to jail when you go to see him in Chapter II regarding the two books needed for the quest A Mysterious Tower. However, you can bail him out for 200 , then visit him at his home to obtain the books. The books cost 400 otherwise.
Killing the Scoia'tael allows you to ask Haren Brogg about Hoog, Zoltan's Scoia'tael friend whom the dwarf had mentioned he was supposed to meet in the Outskirts, but you do not get any information out of it. One of the Scoia'tael also has four Beggartick blossoms on him.
If you save Abigail, she fights with you against the Beast. If she lives, you will meet her again in Chapter IV and she will also help you fight in the Epilogue.
If you do not save her, she dies and you face the Beast with a bunch of villagers. But having sided with them, you will not have to fight them after the Beast encounter. Also, a generic healer will be in the healer's hut in Chapter IV and you will have to fight Abigail in the Epilogue.
Your choice in this decision alters the way in which The Heat of the Day quest in Chapter IV plays out as well because this decision impacts whether you are someone who stays out of other people's business or tries to help others by getting involved.
Decision: Fight alongside Siegfried or alone in the sewers
Choosing to join forces with Siegfried will allow you into the dike with the minimum of trouble and the Order armourer will be willing to deal with you. There will be a generic guard at St. Lebioda's Hospital, and he will let you enter only if you have the City Guard signet ring or with a bribe of 30 .
Choosing to kill the cockatrice alone will let you walk into the St. Lebioda's Hospital with the minimum of trouble. However, the Order armourer will not deal with you but the Dwarven blacksmith will if you helped the Scoia'tael. The guards at the gate to dike will let you enter only if you have the City Guard signet ring or with a one time bribe of 60 .
Decision: Visit the detective right away or start the inquiry on your own.
Consequences: This is only relevant if you let the Scoia'tael take the supplies in Strangers in the Night. Coleman dies immediately after Geralt visits Raymond, which would prevent the player from starting The Rat quest (it is a minor side quest with zero plot impact).
Decision: Side with the Scoia'tael or the Order, or remain neutral (refuse both).
Before Force Recon your actions regarding Haren Brogg's crates in Chapter I may cause the dwarves not to deal with you.
After Force Recon, whomever you choose, the other side is not too friendly with you back in town.
If you choose the Scoia'tael, the order merchant/armourer will not interact with you.
If you remain neutral (by not starting Force Recon) — your relationship with both the order merchant/armourer and the Scoia'tael blacksmith will effectively be reset and you will be able to interact with both of them until you progress farther into the story.
If you side with the Siegfried, the Order will fight with you during the battle.
Opposing a faction during Gold Rush will bar access to their associated path in Chapter IV (e.g. if you help Yaevinn escape the bank during Gold Rush, you may only choose the Scoia'tael or neutral paths in Chapter IV; likewise, helping the Order during Gold Rush will only permit choosing the Order or neutral paths in Chapter IV).
Order path: The Scoia'tael will be enemies in Chapter V, you will be asked to kill more Scoia'tael than White Rayla, to make the armor, you will need to see the Order Armorer and get Saint Gregory's litany. Siegfried will fight with you through Vizima in the epilogue. You will have to fight the ghost of Yaevinn in the epilogue. Sex card available is White Rayla's. You will also be able to receive the Raven's Armor of the Order in Chapter V which gives a huge Vitality bonus (+150) and bonus to Vitality regeneration in addition to -30% damage.
Scoia'tael path: The Order will be the enemies in Chapter V, you will be asked to escort some refugees to the hospital and to make the armor, you will need to see the Dwarven Armorer and get the Bifunctional fiber and alloy recirculator. Yaevinn will fight with you through Vizima in the epilogue. You will have to fight the ghost of Siegfried in the epilogue. Sex card available is Toruviel's. You will also be able to receive the Raven's Armor of the Elves in Chapter V which gives an Endurance bonus (+25) and a bonus to Endurance regeneration and Sign Intensity in addition to -20% damage.
Witcher / neutral path: Both the Order and the Scoia'tael will be the enemies in Chapter V, you will be asked to escort some nurses to the hospital and to make the armor, you will need to see Kalkstein and get Agnes of Glanville's Magic Formula. Triss will fight with you through Vizima in the epilogue. You will face both Siegfried and Yaevinn and depending on your answers you will fight them or part in relative peace; in the Ice Plains, you have to fight their ghosts. Sex card available is for two nurses. You will also be able to receive the Raven's Armor in Chapter V which gives modest bonuses to Vitality (+75) and Endurance (+15) as well as a small bonuses to Endurance and Vitality regeneration and +25% resistances, in addition to -20% damage.
If you save her, you will get the steel sword, D'yaebl and she will fight with you in the epilogue as the Striga.
If you kill her, you will be able to make a Striga's Urge potion using her heart (gives 1 Bronze and 1 Silver Talent) and Vincent Meis will fight with you in the epilogue as a Werewolf, unless you killed him, then Count de Wett will fight with you.
If you refuse, by answering "This is between him and me", then you will fight the King of the Wild Hunt who summons some wraiths for backup. You can collect the unique ingredient for wild hunt vapors from its remains, but only providing you kill him far enough from De Aldersberg.
If you accept, then he does not fight you (meaning less experience) and he tells you that you knew Jacques under another name, but never specifies what name that was.