I generally prefer the horizontal knuckle strike (with first 2 knuckles). However I believe all these strikes are intended to do different things.
The small knuckles do line up better with the wrist, but unless you hand is well conditioned I would not punch anyone in a bony region with this. (try hitting a tree with this part of your hand - you'll find the knuckles have a tendency to seperate). Also, it is possible to line up the first two knuckles with your fist (otherwise you'll break your wrist - a common fighting injury). Also the first two knuckles tend to be more pronounced, and therefore you are more likely to be able to concentrate the force in a smaller area.
When striking with the knuckles horizontal the shoulder tends to turn over and raise making it is easier to direct force from the shoulder. This is also possible with the vertical method, but is less comfortable. The vertical method tends to be faster, harder to see or block (as there is less tendency to do it with a roundhouse style), but less powerful (as it is harder to get the body behind it). Obviously power and speed in either can be developed.
Striking with the fingers at 45 deg, or using a protruding middle finger is usually used for striking pressure points (as a normal fist will not get correct entry as it squashes the surrounding tissue around the pressure point). They are very effective if you manage to hit the spot right, as you don't need much force - whether you can do this through clothing and whilst the opponent is moving is another question.
Its interesting that Wing Chun was developed by a Nun, as it would seem that a female would be better to take advantage of speed rather than body power to strike someone.
For me, I attack with the two knuckle version, and often atemi with this as well because I'm used to it (although my favourite atemis are with pressure points or open hand)- however I would probably be better off using a fast vertical knuckle strike for an atemi.