A lot of junctions in Edinburgh don't faze me over much, partly owing to the number of times I use or don't use them and thus governing the exposure I have to other vehicles. But there are some contenders nonetheless.
1) Calder Road roundabouts. All three of them, and particularly when going straight across north or south. I use the Saughton-Longstone one a lot, and it even has a manhole cover right in the way of primary in the nearside lane.
2) Gilmore Place to Leven St junction. I hate this with a vengence. You risk getting struck by vehicles entering Gilmore Place. Unless first in line you have to wait for all the vehicles exiting Tarvit St to Gilmore Place, and they have a longer green light phase than the traffic exiting Gilmore Place. I'm frequently stuck at this stupid horrible junction for two cycles of the traffic lights. Oh yes, and the surface shakes my bike to pieces as well, regardless of secondary or primary position.
3) Cameron Toll gyratory. Seems worst on the Peffermill-Old Dalkeith Rd-Lady Rd half, owing to the very tight lane markings and lack of time to change lanes, though statistically I think it may be on the safer end of the spectrum.
4) Braid Road/Braidburn Terrace mini roundabout. I have had more "near-misses" at this junction than anywhere else in Edinburgh, even the Calder Road. Carries far too much traffic and has unwritten rules of engagement that seem to favour northbound vehicles above the conventional give way criteria. You also get blinded by northbound vehicles at night.
5) Haymarket westbound.
6) Crewe Toll roundabout.
=) Drum Brae roundabout. Too much traffic carried on both of these junctions in too many lanes squeezed together.
7) Granton Square. There is too much tarmac to play with and vehicle speeds are just too high, especially those speeding into the junction from the eastern side of Granton Road. The gradient doesn't help westbound cyclists who are trying to get from Lower Granton Road to west Harbour Road.
8) Turning right from Bristo Place into Teviot Place. Did they put all those metal studs on the road just to trip up all the cyclists or something?