To avoid spoilers, I'll just list the name of the quests.
The ones with the * next to it involve helping the Thieves guild
Should be safe (does not require a side to be taken):
Search for Andor* (so far)
Breakfast bread
Rats!
Missing husband
Rat infestation
Fallen friends
Key of Luthor*
Drunken Tale
Calomyran secrets
Ancient secrets
A lost potion*
Trusting an outsider
Uncertain cause
Well rested
No weakness
Deep Wound
Devastated land
Lost sheep
Bits and pieces
An involuntary carrier
I have it in me
Currently neutral but involves breaking the law so could have consequences later on:
Disallowed substance
Lost treasures
Night visit*
Kaori's errands - requires completing the Disallowed substance quest
Spies in the foam
Requires you to choose a side:
Missing pieces
The agent and the beast / Clouded intent - these are kind of intertwined and involve the Blackwater Mountain Settlement and Prim dispute. You can also accidentally end up choosing not to help either side, which means you won't get to start the "Lights in the dark" quest. There is also a choice even after you choose a side
Cheap cuts
The path is clear to me
Feygard errands
Flows through the veins
Of mice and men
The dark protector
Everything in order
The five idols (can't be started without choosing a particular side in "Everything in order")
What is that stench? (can't be started without choosing a particular side in "Everything in order")
Can't be started without completing another quest that requires choosing a side:
Lights in the dark - have to complete "The agent and the beast" & "Clouded intent" and have chosen a side
The five idols / What is that stench - have to complete "Everything in order" and which side you chose determines which quest you'll get
A difference of opinion - have to choose to report whether or not you found anything at the cabin near Remgard, in order to enter the town (either choice lets you enter).
Old friends? - have to complete "Missing pieces" (whichever side you chose, this quest will end the same, although it might require less travelling back and forth depending on who you sided with). You also have to complete "Everything in order" to get to where this quest starts.