For those of us who still enjoy the ease of use of the Arduino, but wants a more complex environment, there is MariaMole.
MariaMole is an open source project creating a more advanced Arduino IDE. It complements the existing Arduino IDE and maintains the good parts of the classic IDE (i.e. Arduino libraries, ease of download, etc). At the same time, it can handle multiple projects at once, multiple simultaneous serial port sessions, etc. You can also tweak the the build process for better control.
The only limitation is that it is tied to the Windows platform for now, so now we only need someone to port it to Qt for portability :-)