Check your fluid level. If it is abnormally low, you may have a leak. Also, if the reservoir is completely empty, you may have to follow special procedures to bleed your master cylinder and/or ABS pump.
You will want to bleed your brake system until you have completely replaced the old fluid with new fluid. If you routinely bleed and maintain your brakes, this is not always necessary. But if you do not know the last time your fluid has been completely flushed, I recommend this highly. Brake fluid is cheap and a power bleeder makes the job easy (I think I answered another question of yours regarding power bleeders).
While bleeding check for any leaks around the lines and calipers. You can also pull the calipers off and check your pad wear.
If, after bleeding, the pedal is still soft - I'll just say I've had this scenario on 3 different vehicles and on all 3 it turned out to be the master cylinder. I can't tell you how to tell for sure if this is it. I simply swapped it as the next step after a couple of bleeds failed to fix the problem.