Steve Jones has gotten source level debugging in Eclipse to work with Contiki. This is based on Mar's long work of getting OpenOCD running. From his announcement:

If you're not familiar with Eclipse/CDT see the Yagarto reference. You can
import the entire Contiki source tree into eclipse/CDT in two snips. The
make build is identical to a console build. You just need to point
eclipse at the make file and create a few make targets:

clean TARGET=redbee-econotag
all TARGET=redbee-econotag