Preheat oven to 325°. In a large, wide ovenproof pot, brown bacon over medium-high heat, 4 to 5 minutes. Add onions and garlic; cook until onions are soft, 5 minutes.
Rinse sauerkraut well in a colander; squeeze out as much moisture as possible. Stir sauerkraut into onion mixture. Add 1 1/2 cups wine, the broth, bay leaves, juniper berries, and 1/2 tsp. pepper. Bring to a boil, then cover and bake until sauerkraut is barely tender to the bite, about 1 hour.
In a small saucepan, boil shallots in remaining 1/2 cup wine until liquid is reduced by half. Remove from heat; whisk in lemon juice and mustard, then 6 tbsp. olive oil in a thin stream. Season with salt and pepper and pour into a small pitcher.
Rinse fish, pat dry, and sprinkle all over with salt and pepper. Heat remaining 2 tbsp. olive oil in a large nonstick frying pan over medium-high heat. Cook fish, skinned side up, until browned on the bottom, about 6 minutes.
Nestle sausages into sauerkraut mixture and top with fish, browned side up. Cover and bake until sausages and fish are opaque but still moist-looking in center (cut to test), about 10 minutes.
Transfer fish and sausages to a warm plate. With a slotted spoon, mound sauerkraut on a warm platter; discard braising liquid. Tuck chunks of smoked salmon into sauerkraut and arrange fish and sausages around and on top. Sprinkle with chives and serve with vinaigrette.
*Find at gourmet markets and seafood shops (you might have to order ahead). Or substitute 1 1/2 lbs. peeled deveined raw shrimp (16 to 20 per lb.; tails left on); in step 5, stir shrimp into sauerkraut before adding fish.
SAUVIGNON BLANC: Rochioli Sauvignon Blanc 2007 (Russian River Valley; $26). Rich and complex; lively herbs; exotic mix of Asian pear, grapefruit, lemongrass. Signaterra (by Benziger Family) Shone Farm Vineyard Sauvignon Blanc 2007 (Russian River Valley; $26). Lovely new-mown grass and herb aromas followed by a splash of grapefruit.
SPARKLING WINE: Gruet Blanc de Blancs 2004 (New Mexico; $25). A delightful sparkler with fresh grapefruit, melons, and pears over faint tropical notes. Schramsberg Blanc de Blancs 2005 (North Coast; $36). Crisp apple and creamy lemon blend with stone fruit and a yummy toasted character.
DRY RIESLING: Claiborne & Churchill Dry Riesling 2006 (Central Coast; $18). Fuzzy apricots and peaches balanced by minerals and a touch of classic Riesling diesel-fuel quality (a good thing). Trefethen Family Dry Riesling 2007 (Oak Knoll District, Napa Valley; $22). Crisp and bright, with lemon zest and beautiful stone fruit.
DRY GEWÜRZTRAMINER: Londer Dry Gewürztraminer 2007 (Anderson Valley; $26). Perfumed with honeysuckle and juicy with stone fruit and citrus. Stony Hill Gewürztraminer 2006 (Napa Valley; $21). True to its name—full of wet stones, plus flowers and spice and satisfyingly bitter grapefruit.
Note: Nutritional analysis is per serving.