Is there any way to do queries in postgis using multiple cores in a transparent way, other than splitting my queries among several client connections ?
The quick answer is that you can't do parallel queries. Not yet, at least.
PostgreSQL, the most common database engine that processes PostGIS queries, has parallel query execution as a development priority. Although there has been some progress on the prerequisite background worker API in versions 9.3 and 9.4, the timing of this feature is probably not expected for at least a year or more.
pgpool-II is a middleware that offers parallel query, although I'm not sure if or how it can be configured for PostGIS.