Hard to say, but since you replaced the tranny mount and it didn't fix the issue, then it's not that. While under the car did you check the engine mounts, but I really doubt it's that. Can you explain a little better what the sound compares to, and when it actually happens? Can you feel it in the shifter, if so how does it shift? Is it hard to go into gears, if so try aligning the shifer as it might be this easy??
Do you hear/feel it all the time, or is it only those gears? Does it make any dif as to how you shift-slow/fast.