What is the proper way to format a multi-line dict in Python?

Since your keys are strings and since we are talking about readability, I prefer :

mydict = dict(
    key1 = 1,
    key2 = 2,
    key3 = 3
)

First of all, like Steven Rumbalski said, "PEP8 doesn't address this question", so it is a matter of personal preference.

I would use a similar but not identical format as your format 3. Here is mine, and why.

my_dictionary = { # Don't think dict(...) notation has more readability
    "key1": 1, # Indent by one press of TAB (i.e. 4 spaces)
    "key2": 2, # Same indentation scale as above
    "key3": 3, # Keep this final comma, so that future addition won't show up as 2-lines change in code diff
    } # My favorite: SAME indentation AS ABOVE, to emphasize this bracket is still part of the above code block!
the_next_line_of_code() # Otherwise the previous line would look like the begin of this part of code

bad_example = {
               "foo": "bar", # Don't do this. Unnecessary indentation wastes screen space
               "hello": "world" # Don't do this. Omitting the comma is not good.
} # You see? This line visually "joins" the next line when in a glance
the_next_line_of_code()

btw_this_is_a_function_with_long_name_or_with_lots_of_parameters(
    foo='hello world',  # So I put one parameter per line
    bar=123,  # And yeah, this extra comma here is harmless too;
              # I bet not many people knew/tried this.
              # Oh did I just show you how to write
              # multiple-line inline comment here?
              # Basically, same indentation forms a natural paragraph.
    ) # Indentation here. Same idea as the long dict case.
the_next_line_of_code()

# By the way, now you see how I prefer inline comment to document the very line.
# I think this inline style is more compact.
# Otherwise you will need extra blank line to split the comment and its code from others.

some_normal_code()

# hi this function is blah blah
some_code_need_extra_explanation()

some_normal_code()

I use #3. Same for long lists, tuples, etc. It doesn't require adding any extra spaces beyond the indentations. As always, be consistent.

mydict = {
    "key1": 1,
    "key2": 2,
    "key3": 3,
}

mylist = [
    (1, 'hello'),
    (2, 'world'),
]

nested = {
    a: [
        (1, 'a'),
        (2, 'b'),
    ],
    b: [
        (3, 'c'),
        (4, 'd'),
    ],
}

Similarly, here's my preferred way of including large strings without introducing any whitespace (like you'd get if you used triple-quoted multi-line strings):

data = (
    "iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAYAAAAf8/9hAAAABG"
    "l0RVh0U29mdHdhcmUAQWRvYmUgSW1hZ2VSZWFkeXHJZTwAAAEN"
    "xBRpFYmctaKCfwrBSCrRLuL3iEW6+EEUG8XvIVjYWNgJdhFjIX"
    "rz6pKtPB5e5rmq7tmxk+hqO34e1or0yXTGrj9sXGs1Ib73efh1"
    "AAAABJRU5ErkJggg=="
)