I am just back from a week trip to Chisinau, capital of Moldova. It was hard to find good accommodation in the center city at a reasonable price - hotels are very expensive and most of poor quality. So I can recommend Svetlana & Daniel's apartment which I found finally. They have website http://www.chisinau-moldova.com
very friendly, helpfully and they must have the best quality/price in the city

If I was going to Chisinau, I'd stay in Iasi, Romania. It is an amazing city!