I've been thinking and thinking on this. I guess it's a good problem to have that narrowing it down to three is impossible. It depends on my mood - am I in the mood for culture/history/city or natural beauty/serenity/mountains/ocean? It is really tough to say! The world really is an amazing place.
For sheer natural beauty, I guess I'd have to say:
1. Patagonia (both Argentina and Chile - the El Chalten and Torres del Paine areas both blew me away)
2. The Maldives (I haven't been since 1984 so my memory is of a totally unspoiled atoll paradise; not sure if that would hold true today or not)
3. Galapagos Islands (the sheer volume of animals and how unspoiled and untouched it all is, plus the diversity in landscapes amongst the islands)
Runners up - Moorea, S. Island of New Zealand, Bali, Yosemite Valley and the Vincentina Coast of Portugal. I'm headed to Bryce Canyon and Zion NPs in a week and suspect they may be right up there too!
For history/culture:
1. Italy (not one specific place, but the mix of the small hill towns with places like Florence & Rome is hard to beat)
2. Turkey (Istanbul is such an amazing mix of history/culture/modern city plus the ruins at Ephesus are the most amazing I've ever seen)
3. Greece (this one is more of a mix of nature and history, plus I just love their food and their lifestyle)
Favorite cities:
1. Lisbon
2. Amsterdam
3. Hong Kong
These might be my favorites because I know them so well. I lived in HK as a kid, studied just outside Amsterdam in law school and have a house not far from Lisbon now. To me, the measure of a great city is one that you fall more in love with the more time you spend there, and all three of these are this for me.
Runners-up (San Francisco, London)