1. It will soon be Malaysia - Kuala Lumpur as the legislative capital and Putrajaya (sp) as the administrative capital
2. Bolivia may qualify. As far as I know, some parts of the federal government are located in Sucre, although of course La Paz is the main capital.
3. The Netherlands:
The Hague:
Seat of the Dutch government and parliament.
Royal residence (Palace "Huis ten Bosch") of Queen Beatrix of the Netherlands and her (late) husband Prince Claus of the Netherlands (who sadly died yesterday 6th october at the age of 76).
Seat of the provincial government of the province Zuid-Holland.
Amsterdam:
Capital of the Netherlands where since 1815 all Dutch monarchs are being 'crowned'.
4. Tanzania (Dodoma/Dar es Salaam)
Ivory Coast (Yamoussoukro/Abidjan)
Kazakhstan (Almaty/Astana)
Germany (Berlin is the capital while some part of the government stayed in Bonn)
link:
http://www.airliners.net/aviation-forums/non_aviation/read.main/288848/