The average cyclist does not have an unlimited budget when it comes to upgrades and a common question is where is the "best" place to put limited dollars.  One of the first things to consider is how long to you anticipate owning your bike.  There is no point in sticking a lot of money into a bike you will likely sell in a year or two.  If this is the case purchasing components that may transfer to a new bike makes more sense.  The following top five not only represent the best return on investment, some will also transfer to your next bike purchase if need be increasing their value even more.

• Shoes- Moving or inertial weight is what you want to reduce foremost and it requires energy to move.  Shoes are never factored into the advertised weight of a bike but they represent a lot of moving weight.  I have had athletes drop over half a pound with a shoe upgrade under $150.  It is important check the weight of carbon soled shoes against other composites.  In some cases I have found that the carbon sole version of the same shoe weighs several ounces MORE per shoe than the less expensive version.
• Helmet- The head represents a lot of drag producing surface area.  Upgrading to a more aerodynamic bike is very expensive and the drag reduction is still pretty small.  Many of the new helmets are wind tunnel tested to reduce drag without hindering cooling.  Besides you should replace your helmet ever 5-8 years depending on wear and their are new safety technologies such as MIPS and better fit systems.  A new helmet is a good investment especially if it is past the expiration date.
• Pedals- Like shoes pedals are inertial weight, and if you are on a dated alloy pedal upgrading to a composite pedal represents a good return.  Pedal bearings wear out over time and if you can grab the pedal and move it on the spindle yours are probably worn.  Some bearings are serviceable but most are not, and even the ones that are rarely get the required attention in my experience.  Pedals also come with new cleats which may help limit movement/play in your pedal stroke.
• Saddle- I am always amazed at how long cyclist needlessly suffer the pain and discomfort of a stock saddle.  Finding the right saddle can be somewhat trial and error but once you do it can make a huge difference in your riding enjoyment.  An uncomfortable cyclist does not produce as much power; a saddle is a performance upgrade as well as a comfort upgrade.
• Fit- Although a fit will not transfer to a new bike a good fit will allow you to ride longer, more powerfully, reduce drag (perhaps significantly), and prevent injury.  If you received a cursory fit, or ride a bike you purchased used with no fit, this can be the biggest and most significant performance upgrade of all.

These are the places I recommend spending your money on first and then you can move on to much more expensive components such as a crankset, wheelset, or carbon whatnot.