Just to add to the Laynes, Mrs Athas, La Botega list.... (all of which are flawless in my book)
Fika North on the top side of headingley is superb (using Casa Espresso)
Salami and co in Otley make an exceptional Long black.
Kapow (Call Lane) do some good coffee although slightly bitter for my tastes) and slightly dependent on which Barista is in on the day. I like it because I can park out side for 30p and dash in on the way to the M1.....
Opposite in Chapel A used to be my 'go to' but they downgraded from premium beans to NorthStar, they remain passable, and they do guest beans on batch brew.
Broomfield Square in Otley is surprisingly good. not an out and out coffee venue but the guy in there seriously knows how to brew! One of the few places I have bought a second cup before the first cup went cold (Laynes being the other).
Stage espresso. Pretty good, but I would probably walk the extra 200m and go to la Botega.... nice for a change though.
Lots of people love Northstar in Leeds Dock, but I find it a little 'ordinary'. The beans are mid range in price and I think that shows in the coffee (Confirmation Bias??)
Lots of other people like Wolfox or wolf fox?? near the station, but I have had some really over-extracted brews there and the Barista told me 'I must be mistaken' while I spooned in sugar to make it drinkable. I also heard the guy who runs it 'slamming' some of the other places on this list for using 'blends'. I didn't really appreciate his attitude.