Recently a colleague of mine ran into the issue where she has more than one instance of SQL Server running (of course on different ports), able to connect with SQL Mgmt Studio, service instances running fine but JDBC applications are not able to connect – encounter an “…jdbc.SQLServerException … Connection refused …”
- Learnt that the SQL Browser Service has to be running - this is not required for a single instance. Multiple sql server instances need the sql browser service to be running for proper connection from clients
Did not find many links related to this when trying to fix the problem 
but searching for sql browser service and jdbc now brings up some useful information
http://www.mssqltips.com/tip.asp?tip=1946
http://msdn.microsoft.com/en-us/library/ms181087.aspx (via http://bytes.com/topic/sql-server/answers/808470-sql-server-browser-service)
