Same as it does now, multiple ports on the right edge - except they would be mirrored along the bottom edge too.
These doesn't always be visible, only when the node is selected, with the mouse nearby or above.
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I am thinking something more along this:
If the x coordinate of the default output position (the red line) is equal to or smaller than the x coordinate of the default input position, then use the default positions (A), else move the output to the bottom and the input to the top (B).
Still have to figure out a usable logic for when there's multiple nodes connected to each input/output, though.
(Sorry for the MS Paint "artwork")
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oh wow there is alot to this visual vertical discussion. 
just some 2c. Could both vertically and horizontally wires be enabled so you have a mix based on what you want to do.
But maybe the thought here is (individually control that on the Node itself. when you place the node- say you want to flip the orientation vertical/horizontal you click node and a ticker box states oh flip it vertical from default horizontal.
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Every wire would require an additional port location meta info, not very practical and not intuitive visually when input is at the top and output on the right like that.
If anything, have a v flag in each node that it's vertical, or inherit that from groups & tabs ?
Mixing horizontal and vertical would be a great option imo, a checkbox or dropdown in the node properties to set vertical or horizontal mode would do it for me.
I'm enjoying this discussion and am curious to what may be ultimately decided upon. Thank you all for taking the time to put forth new ideas and the node-red developers for managing expectations by highlighting the implications.
I do like the idea of a per node switch, with a per flow master that defaults newly added nodes but leaves existing nodes as-is.
I have many flows with lots of mini flows on each, so one size fits all would not work for me. But I can see in some of my flows where vert would work for nodes with multiple outputs.
Also, adding the option per node would mean existing nodes would be unaffected and importing flows would follow whatever their setting was (default horiz).
