If I only had two, I'd probably choose Paris and St. Petersburg.
Both are simply breathtaking, but Paris' architecture, character, food and atmosphere is unique, and very accessible in a short time (it's actually a surprisingly compact city). Well, there's nothing I can say that hasn't already been said: it's Paris FFS!
St. Petersburg, however, is in my humble opinion, simply magical - my favourite city in the world. Built by force of will by a singular teutonic individual to bring Russia into Europe, it is finally emerging from a century of decay (thanks to Putin and his clique of Leningraders) but has yet to become too gentrified. It is simply breathtakingly beautiful - full of canals and pastel-coloured stucco structures mingling with Russian Orthodox 'kupelleh' churches. It also happens to house The Hermitage - hands-down the single most amazing museum in the world.
For others:
If you go to St. Petersburg, I'd also advise you to include Moscow - St. Petersburg's evil twin. It is said that Russia is a bipolar country - with St. Petersburg and Moscow as the two extremes. An overnight sleeper-train trip connects the two, and Moscow's brashness, confidence, ostentation and dynamism together with its incredible modern history makes it a very interesting counterpoint to St. Petersburg's introspective majesty...
If you want another stop-over en-route back home, I'd also advise a weekend in Reykjavik, Iceland. TINY, but with one of the best nightlifes in the world, the country was a total surprise the first time I went five years ago. I've been back four times since! Windswept, devoid of vegatation (it is covered only by moss), and covered in fjords and lava fields, the country is like an alien landscape - just populated by the most wonderfully eccentric and friendly people. It also happens to be cheap thanks to an economic crisis, and Iceland Air is offering special packages from the UK to the US including a stop-off in the capital. Well worth it to get off the beaten track IMO...
There are more, but if I was choosing, these are the ones I'd choose (and I'm a Londoner and am not including it). I think they really gives an idea of the artistic, intellectual and physical differences in what is the world's smallest continent.
(I've been many times to Prague, and just got back from a trip to Tuscany - Siena, Luca, Florence etc. They're all nice, but I always get the feeling they have become pastiches of themselves. Those I've written above, more than anything else, are living, breathing cities in a way that none of the interesting parts of Prague or Tuscan Italy are... Just my $.10)