We spent two weeks in Croatia in March - following is a link to our (unfinished) blog

http://lizandrichardsa.typepad.com/parisandbeyond/croatia/

(check back for updates and more restaurant info)

We stayed in apartments - highly recommend the apartment in Dubrovnik - lovely owners/fabulous view and parking (that's really important in Trogir and Dubrovnik)

http://www.dubrovnik-accommodation.net/index.html

We stayed in apartment A2.

There is also a new hotel in Dubrovnik - fits your description of boutique I think

http://www.villa-dubrovnik.hr/

There is a 'boutique' hotel in Sarajevo...

http://www.cityhotel.ba/

It looks very nice on the website, but I don't like the very busy street it is on - and I'd imagine if you had a room overlooking the street it would be very noisy with all the trams, buses and cars going along it on the oneway system.

There is also this one, which is a bit further up the hill from where I stay, and I definitely prefer this location...

http://www.hb36.ba/english.html

I stay at the Hotel Safir - not a boutique hotel, but very clean with fantastic service and a terrific location...

http://www.hotelsafir.ba/engleski/index.php

I was in Sarajevo just last week (and Mostar too) and if you click on my name you'll find links to my current and previous trip reports about visits to this beautiful and relatively undiscovered part of Europe.

Check out Hotel Michele in Sarajevo. We loved t.

We drove from Dubrovnik to Mostar and Sarajevo then back down to the coast and north to Istria. There were no problems on the borders. A beautiful place to visit in Croatia is the Peljesac Peninsula which is famous for its wine. On the way to Mostar you will pass the village of Poticeli which is worth a visit. At Sarajevo we stayed at the Hotel Bosna at Ilidza on the outskirts and caught the tram into the city each day. This was recommended to us by someone in Dubrovnik and it was very good advice. Two of the best places we visited in Sarajevo were the History Museum and Imat Kuca restaurant (authentic Bosnian food and music, right beside the river opposite the National Library). In Mostar the museum is very interesting. We also took a drive to Stolac and the Hutovo Blato National Park. It was through back roads with signs on the side of the road warning of landmines.
It's a great decision to visit Bosnia, especially with a car.
http://www.travelmagpie.com