Sorry, let me redo those pictures....

the house
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Here's a picture of the master bedroom (also, would you keep those shutter blinds?)
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Here's the staircase (what would you do with the banister? paint it? stain it?)
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and a picture of the office
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and a picture of the family room with parquet floors
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I love colonial homes, that's what we have too. I also love dark floors, we put oak throughout the first floor except the kitchen & dining room, which has Brazillian Walnut. We opted for the dark floors because they look better with our oak cabinets. Unfortunately, we did the kitchen last and if I had known how wonderful the dark floors were, I would have opted to do the whole floor in the darker wood. That said though, I love the oak as well, it matches the style of the home better which was our intention. Just my personal preference, but since the home is traditional in style, I'm trying to keep the interior more traditional as well and the darker floors have a more contemporary or modern feel to them.

I like medium dark wood floors. The cherry or even
saddle brown is wonderful. But I agree with Lukkiirish
that dark can have a modern appeal. I have seen some
amazing dark chocolate floors. It is a hard choice.

Do you have a lot of light in this home?
From the pics it looks like you do.

The shutters are fine if you are keeping the floors
the same color. Otherwise paint them white. You mentioned
painting all the trim white. This will definitley
update your place and have a clean feel.
Do you prefer white to wood?

Here are some inspiration pics that may be able to
give you and idea of what color to stain.
I myself am in the same boat as we are changing
our honey oak floors to a darker color.

I am not saying to do this color, just giving you
an idea of a dark color.

Lighter floors are pretty too. Something to think about.
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Dark Parquetry
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Wood with white trim is just lovely.
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My current favorite among readily available stains is MinWax's English Chestnut. It is rich and deep without being gloomy, and adds depth and structure to a room.
In your house, I would paint all the dark wood white (or a version of white), and colorwash/sponge the brick wall with a wash of a soft stone color. I'd paint all the walls the same white as the trim, to give myself a fresh clean starting point, and wait to choose final wall colors, until I could see the place and the light and my things in it from that starting point.