I don't know about always being pegged as a tourist. We've been approached by people speaking to us in Russian, Romanian, French, Italian, German, etc., expecting us to understand them and be able to respond like a local. We don't usually take any jeans, they're heavy, hot, hard to wash and dry, take up too much room/weight in a suitcase, etc., etc. Dockers/casual slacks in any color darker than a very light khaki work well. Even some of the microfiber Dockers - lighter, cooler, don't wrinkle much. Europeans still do wear a lot of black as their base color. Your black Nike's will be fine, as long as you can walk miles in them. Take some blister packs, maybe moleskin, and a small roll of tape, if this much walking is unusual for you. Collared, woven shirts will be good, short sleeve or long. Solid color T-shirts would be good, too. Fred Meyer has some good men's T-shirts in solid colors with chest pockets, not expensive. Simple dark jacket. A "windbreaker' will peg you as an American tourist.
You will likely get both cool/cold and warm weather then in those places. Layer, take a lightweight fleece jacket under your light waterproof jacket. Same for your girlfriend. Have her wait and buy pretty, fake "Pashmina" scarves there for warmth, lots of pretty colors available cheap. For her - walking shoes like trail shoes or Nikes or something, plus a pair of comfortable flats she can walk in. Some flats that have some cutouts on them can double as almost a sandal. Generally darker, more drab colors will let you blend in. Backpacks will scream tourist, but so what. For your girlfriend - I recommend travel purses from PacSafe. They make a not-too-big one which works great as a cross-body purse. All steel reinforced, but not at all heavy or bulky. Good pockets, clips to secure zippers, etc. Many years of traveling and they're the best I've found. I never let go of my purse, and these can also be attached to a chair, etc. for security. My departures from drab colors are usually a scarf, my purse and daypack (I want to see them in a crowd if they do get away from me) and my mini-umbrella, so I don't just look like everyone else with black umbrellas. If it's just the two of you, it isn't as important, but in a group it helps.
For her - take a couple pants - synthetic-blend, non-wrinkle decent slacks and a pair of something like the Lee or Gloria Vanderbilt pants that are like jeans (5 pocket) but lighter weight twill and stretch blend. Black. And maybe a microfiber capri. I also spend my time on the plane and long trains in a pair of lightweight stretch knit pull-on pants. Something comfy that bends. Then a couple skirts, one below the knee, other can be short (a skort is safer), if it gets warm. One pair of tights under a skirt for in-between weather, if wanted. Tee shirts and a long sleeved shirt that doubles as a light jacket and a light cardigan sweater, like the Land's End or LL Bean pima cotton type.
One thing you will find out is that clothes can really take a beating while traveling and wearing them a lot. They do show wear. I've learned NOT to pack my favorite clothes for travel, as they can get ruined or worn out. I pack something functional, but that I don't care so much about. Especially pants. T shirts - I've been known to buy a few in solid colors cheap somewhere and throw them away at the end of the trip when I need room for souvenirs. Got a bunch for $4 each before one month-long trip, wore them out and tossed them. (Wash them for color fastness first, though). Ditto with underwear and nightgown. I get those at WalMart and pitch them at the end. No big loss and leaves room for souvenirs.
You'll be fine with just casual work-type clothes. Simple... Plain... Fast drying... Paris could be warm, London possibly still cool and damp. You're used to that, as I am here in the northwest. Don't worry about what you look like, just be comfortable! Bon Voyage!!