I still think that there are two major areas. The first is application support. Application developers (everything from word processing to databases to games) have been slow to adopt Linux as a platform. A lot of this can be attributed to the economic climate over the last three years, but at least some of it is attributable to the second area of development need.
The second is ease-of-use/ease-of-administration. Although the desktop environment (either gnome or CDE) has gotten much better, there are still major issues with configuration and administration. Simple things like configuring X-Windows still requires considerable knowledge under certain circumstances. Adding devices and device drivers can still challenge the most adept administrators. Configuring a Linux firewall, for example, is quite a challenge.
Better documentation and better GUI interfaces will make a huge difference, but these things take a lot of time and effort. It is getting there, it just has a way to go."