I do eyes based on how deep I want the fly to go and how fast I want it to get there. Eg. I have used the large sized tungsten eyes from Orvis on #4 and #6's for getting shad flies really deep really fast and I've used bead chain eyes on #2 and #0 for more delicately landing flies for spook-prone reds in shallow water. For cones, it is sort of the same deal, but you also have to take the size of the hole into account to be sure it will fit over the barb if you have one and also around the bend.
For articulated flies, I use 40# mono lashed in a loop to the front hook shank, but I only tie articulated flies for lake stripers and cobia, so they're all on #0-#0/4.