Preheat oven to 375 F and line a baking tray with parchment paper.
Cut squash in half, lengthwise, scoop out seeds, and place, flat side-down on prepared tray.
Poke holes into skin of squash with a fork and bake until tender to the touch, about 35 minutes. Cool, scoop out squash and purée until smooth.
Increase oven temperature to 400 F and grease and flour 36 mini muffin cups.
Melt 3 tbsp butter in a heavy-bottomed saucepot over medium heat, then add flour and cook, stirring with a wooden spoon for 2 minutes.
Whisk milk in a slow stream and bring to a full simmer, whisking until thickened, about 4 minutes. Reduce heat to low and stir in cheese until melted.
Remove from heat and stir in squash, maple syrup, thyme and nutmeg and season to taste. Stir in egg yolks.
Whip whites until they hold a medium peak when beaters are lifted. Fold half the whites into squash mixture until just incorporated, then fold in remaining half.
Spoon or pipe mixture into prepared mini muffin cups to ¾ full. Bake for 15 to 18 minutes, until soufflés have puffed and are golden on top.
They will fall after a minute out of the oven. Serve soufflés warm or at room temperature, with an oven roasted tomato on top.
Oven Roasted Tomatoes:
Preheat oven to 225 °F and line a baking tray with parchment paper.
Cut tomatoes in half and place face-up on baking tray (close together is just fine).
Drizzle with olive oil, sprinkle with sugar, salt and pepper and roast until no longer juicy (but not browned), about 75 minutes. Cool and store refrigerated until ready to use.