I'm in a similar position as you are. I have a 2004 Allez I've been wanting to upgrade. I've upgraded the stem for a better fit, and a seat post due to a crack. But as for the other stuff I'm thinking of holding off. The reason is I want to go full carbon sometime soon. I'm thinking wheels are the smartest choice because that's something you can easily move right over to a new frame. Granted you can switch over a group set as well, but it is a lot of work. Personally upgrading pedals, (unless it's to clipless) is very minimal between low and high end stuff. Handlebars/stems are a similar story unless it's for a fit issue or you're an ultra strong rider who can really feel that sort of difference in stiffness.

Of course better stuff looks cooler too.... haha screw my advice, just do it! I may join you.