Assuming you are limiting the choices to good, reasonably-priced, not necessarily Michelin star restaurants:
Where in Alsace will you be based? Let me know so I can recommend nearby restaurants.
If you go to Riquewihr, try the restaurant of Le Tire Bouchon in the tiny town. Very quaint, typical and traditional and the regional cuisine is done very well - plus, it is very inexpensive. I liked it even better than La Table de Gourmand there (the only Michelin star restaurant in town).
Burgundy: Either staying in Beaune or Saint Romain…Ma Cuisine is a given, Chez Guy and La Ciboulette also…any others that stand out at the moment?
Try lunch at Le Montrachet (in the town of Puligny Montrachet, very near Beaune, you can’t miss it once in the little town). Their dinner is also excellent, but if you are looking for bistro prices, the cost of lunch will be more in the ballpark. Of course, as you already know, Ma Cuisine is a must. I always eat there at least once whenever in the Côte d’Or.
Bordeaux: Le Brasserie Bordelais and La Tupina are the only two I’ve got jotted down here so any tips will be helpful.
Le St-Julien in, naturally, St-Julien (along the main town road, you can’t miss it) - very good food, good wine list where you will find some good prices with a wide selection. Usually a local crowd here. Very good place.
For a quick, simple lunch or dinner, I sometimes go to Lynch Bages’ Café Lavinal in Pauillac behind the château (simple, decent, inexpensive).
Claude Darroze in Langon - if you find yourself around the Gaves/Sauternes area, you simply must eat here. Excellent. FWIW, Parker and Jancis Robinson eat here (though not necessarily together of course) when they are in the area. It’s a bit of a drive from Margaux where I stay when in Bdx, but the drive is well worth it.
Paris: Only three days here…looking at Les Papilles…probably spend most of my time moping around wines bars like Willys, Racines, etc but any solid affordable bistro tips would be awesome.
L’Os à Moëlle (#3, rue Vasco da Gama, 15th Arr.) - solid bistro. You can’t go wrong with the food and the prices are very reasonable. Excellent QPR.
Aux Pied de Cochon - Very touristy with cliché, yet enjoyable, music, a great place to eat and drink very late at night through the wee hours of the morning (it’s open 24/7). Great, super fresh oyster selection, inexpensive prices. Most everyone goes here: after-clubbing Parisian youths, tourists from all over the world, business people (I was actually beside a table of a Parisian couple and their lawyer discussing inheritance taxes here one lunch), you name it. I’ve read Anthony Bourdain likes to “de-toxify” here after a night’s drinking binge. Me? I love having a very late dinner here (11pm onward) and with a couple of bottles with my wife and we just walk back to the hotel laughing like idiots. #6, rue de Coquillère, 1st Arr.
Aux Lyonnais - one of Ducasse’s restaurants, a 1930s style bistro. One of my favorite bistros in Paris. Their versions of oeuf cocotte and veal liver are to die for. Very reasonable prices. #32, rue St-Marc, 2nd Arr.
Le Soufflé - #36, rue Mont de Thabor, 1st Arr., this is one of my go-to places as I always stay in the 1st Arr. in Paris to be near the Louvre. Like Aux Lyonnais, I eat here at least once whenever in Paris. Not a bistro, it’s nicer, but very homey and moderately priced. Naturally, for dessert, don’t miss their soufflés (although my wife likes the savory ones too) - I always have the dark chocolate soufflé and ask them to drizzle a bit of Grand Marnière on top of it.
Café Angelina - For a nice breakfast with great hot chocolate, along the rue de Rivoli, 1st Arr. (across the Jardin des Tuileries, the cross-streets are rue de Algier and rue de la Paix). My wife loves having breakfast or a mid-day snack here.