Accumulator pressure loss
SMG Reprogramming
I have had my accumulator replace twice now due to loss of hydraulic pressure.  Apparently, the accumulators
do loose pressure over time, especially if the car is driven in a fairly 'spirted' fashion.. flat changing, club days, etc..

The most telling symtom is the long 'buzz up' when the the drivers door is opened upon entering the car. 
Typically, after the car has not been driven for a while (say overnight) the hydraulic fliud flows back into the reservior, upon opening the driver's door in the morning there is a 'buzzing' sound as the accumulator pumps the fliud back into the clutch mechanism. 

This should gerenally take up to 10 seconds to complete.  If this takes longer there is fair chance that the pressure is not holding in the accumluator unit.   Another tell-tail symtom is this startup buzzing when the door is opened even straight after driving the car.
As the SMG unit requires this hydraulic fliud to operation the clutch, if left uncheck it can result in non-selection of gears, particlularly 2nd and reverse.

The only fix for this is to replace the accumulator unit which can be quite costly.  
I have had the SMG reprogrammed  twice now..  This is a factory/dealer option which is released with other software updates relating to numerous components and models. 

What the latest program gives you is a slightly quicker change 1st to 2nd but not by much as these still have to work within BMW and local governences.

As enhancements are made to the SMG programs are made by BMW it is sent to each dealer as part of a general software upgrade, who may or may not install this.  In my experiance I had to ask my dealer to install the software when I found out about this as this is generally overlooked.

With the advent of the SMG2 the orginal SMG1 updates are becoming less frequent.  I would suggest that when you next take your car in for a scheduled service, you request that they update the SMG software to the latest version they have...This will not give you "super fast" gear changes but the smoothness and speed improvement you do get will make a difference. 

Cost involved is minimal based on my experiance.
Known M3 SMG Problems
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Info Page
The experinace that I have had with my BMW M3 SMG has not always been the best, most of the problems I have had related to the  SMG.  This page does not only focus on SMG related issues but also the most common problems I have experianced  ..  This said, I believe that this is still one of the most fantastic motor vehcles to drive and own.......

Below are some of the problems I have experinced and the potential remedies that have worked for me.....
Trailing Arm Bushing
What are the symptoms of worn trailing arm bushing?

Generally you will feel a 'squirmy' rear end and experience excessive rear wheel camber (in excess of negative 3-4 degrees) to the point of taking the edge off of the inside of the rear tires.

With worn trail arm bush, one will feel instability at high speeds, cornering and also the car may move around on you in the rear under heavy breaking.  This is caused by constant variation in the rear toe settings which is usually prevented by the properly functioning bushings.

Cost involved in fixing this can vary based on whether OME or after market parts are used.
Vanos Replacement
I had the Vanos unit replaced due the car stalling  for no apparent reason. - SMG car should never stall unless the car has been over rev'ed excessively (ie, circle work or consistent power slides).

After the second stall, I returned the car to the dealer who on investigation found that the Vanos Unit was faulty, the gear assembly had rattled loose.  This is not a common problem but noisy vanos units are quite common.  These are not generally 'picked up' as the M3 engine is noisy.

Cost involved in fixing is quite costly as the whole assembly need to be swapped out.