What is a rule of thumb for when to begin a descent?
Descent planning for jets can get a little tricky at times, and you have pointed out some of the things to look at when deciding when to start down (assuming that ATC gives you the option to choose your own top of descent).

The descent point is dependant on your aircraft and how much drag there is at your descent speed.  Anything that adds more drag allows you to come down faster, but also makes the flight less efficient since you would have burned less fuel had you just started down earlier without the drag.

A typical jet will descend with the engines at flight idle and the speed at the recommended descent speed, which is usually close to the maximum speed for the airplane.  A good rule of thumb for most jets would be:


  3 miles for each 1,000 ft. of altitude to lose + 1 mile for every 10 KIAS of airspeed that you need to lose before landing.


Example:  

We are cruising along at 38 thousand feet and landing at an airport with an elevation of 2 thousand feet which means that we need to lose 36,000 ft.  Let's say that we will be descending at 350 KIAS and need to slow to 150 KIAS for landing:


  Thousands of feet to lose: $38-2=36$ thousand feet
  Tens of KIAS of airspeed to lose: $35-15=20$ tens of KIAS
  
  Distance = $36\times3+20=128NM$ from your destination


So in this case, we will start down 128 miles out.  

There are various factors that can cause this to be a little off, the biggest being the wind.  As the descent progresses, you should mentally double check your progress.  In this case, maybe check when we have 20,000 ft to go (should be 80 NM out now) and when we have 10,000 ft to go (should be 50 NM out now).  

If one of your checks indicates that you are a little off, you can adjust your descent rate (adding a little power or using spoilers to descend more quickly) to get back on track.  

A slight variation of this uses the same calculations, but instead of using the airport as the "target" altitude and speed, they use a point 30 miles from the airport at 10,000 ft above the airport at 250 KIAS.



The above method is enough to get someone started, and just "works" most of the time.  As a pilot becomes more comfortable with the math, they can start to make adjustments for other factors like:


The effect of the winds at the various altitudes during the descent

Headwinds mean that you can wait a little longer to descend
Tailwinds mean that you should start down a little sooner

Weight of the aircraft

The lighter the aircraft, the later you can start your descent.  (If this seems backwards, consider that when you are heavy it will push the airspeed higher faster as you lower the nose and you will have to raise it to keep from overspeeding.  When light, you can keep the nose further down and will therefore have a higher descent rate.) 

The direction that you are approaching the airport from

If you are landing straight in you should start sooner
If you are going to fly a downwind, base, and final, you can start a little later

ATC speed restrictions can prevent you from descending at your normal rate, so you may need to start down earlier.
Inoperative equipment (i.e. spoilers, etc.) may keep you from descending as fast so you may need to start down earlier.


As far as the configuration of the aircraft, in order to get the most fuel efficient profile, I would keep it clean as long as possible and start the descent at a point where I could glide for the majority of the descent and configure on speed for a stabilized landing in the normal landing configuration for the aircraft.  If this is your goal, then the use of spoilers is an indication of poor planning!  ;-)