I've been going to Bergamot a few times a year since it opened about four years ago (five now? how time flies). It generally exceeds the ever-higher expectations I have for it based on preceding visits. The food is subtle, elegant, sophisticated but refreshingly approachable. It's frequently adjusted for seasonality and local availability.
The desserts are deservedly famous. The service is hands-down the best in Boston, and frankly, I can't think of competitors elsewhere, either--certainly not in this surprisingly affordable price point.
Wines are well curated and unique. The list can be tough to navigate even for a more knowledgeable drinker (not long, but with little context the lesser-known offerings get lost), but staff are well-versed and happy to help.
The ambience is cozy, conducive to conversation; no tvs (hallelujah). Good for romantic dinners as well as for business meals, it's just a tasteful, elegant, unpretentious dining room with lovely touches (dessert amuse, gratis sparkling, well-appointed WCs, etc).
There are also excellent bar offerings--their Quebecois is the best almost--Manhattan out there, for my money--and a good late-night menu. It's a neighborhood favorite, a Boston favorite, and there's a reason (well, many of them) that Bergamot is rated #9 *in the country* by Zagat's for New American Cuisine.