some questions I received.

[Navcom]

A1/10@B-25 Lineman A66 drifts downfield because he has no one to block. He is
standing at the B-21 when the pass is thrown. A12 catches the ball at the B-15 and runs
to the pylon where he dives over the GL extended. While in possession, the ball crosses
the sideline at the B-1 and then crosses the GL extended. After the ball crossed the GL
extended but before A12 hit the ground he hit the pylon with his arm. Ruling, Clock?

 A1/10@B-25 QB A10 running an option play to the right. After taking 5 steps to his
right. He pitches the ball from the B-27 to A33 who catches the ball at the B-29. Under
heavy pressure and not having anywhere to run, A33 throws the ball OB and it lands 10
yards beyond the NZ and far OB. ruling? clock?

 A1/10@B-22. B1 intercepts a pass at the B-3 and his momentum brings him into the EZ.
While in the EZ he is hit and fumbles. The fumble rolls forward to the B-2 and in the
multiple players jump on the ball and it is muffed into the EZ where it rolls OB. ruling?
clock?

 A1/10@A-49. The clock is running at 0:35 on the clock. A81 catches a pass at the B-28
and is tackled in bounds at the B-20. As the clock is restarted QB A10 lines up under
center in a hurry up attempt to spike the ball. A10 drops the snap which bounces on the
ground once and he immediately possesses the ball and spikes it to the ground. the clock
reads 0:08... ruling? clock?

[Sonofanump]

1) ball did not "land". 
2) not original to control snap
3) ball did not "remain"
4) ball touched the ground

[Kalle]

1. Ineligible receiver downfield. A1/15@B-30, readysnap. Team B will not decline the penalty as the result of the play is a touchdown.

2. Illegal forward pass (intentional grounding variety). A2/14@B-29, snap.

3. Safety, B FK@B-20. B1 is responsible for the ball last entering the end zone.

4. Illegal forward pass (IG). The foul causes the clock to stop so ZAP-10 applies, and the game is over / extra periods start.

[ElvisLives]

1. Ineligible receiver downfield. A1/15@B-30, ready. Team B will not decline the penalty as the result of the play is a touchdown.

Kalle, as you say, the pure result of the down is a touchdown.  Therefore, after the penalty at the previous spot, the game clock will start on the snap, I believe.

[Kalle]

Kalle, as you say, the pure result of the down is a touchdown.  Therefore, after the penalty at the previous spot, the game clock will start on the snap, I believe.

You are, as always, absolutely correct. I always get this wrong.

[ElvisLives]

You are, as always, absolutely correct. I always get this wrong.

Like you, I work hard at trying "get it right." But, no, not always right (especially with "Replay").

As for the clock, it seems like we can always come up with an 'exception' for something, but, with only very rare exceptions, any time the ball becomes dead behind a goal line (touchdown, touchback, safety), the game clock will next start on the snap.

So, what exception might there be? An illegal pass by team A to conserve time, and thrown from A's end zone, with less than two minutes remaining in the 2nd or 4th periods. Team B may decline the penalty.  and have the ball placed at the previous spot, and there is no distance penalty.  But the timing rules still apply, and the game clock will start on the referee's signal.

[Kalle]

So, what exception might there be? An illegal pass by team A to conserve time, and thrown from A's end zone, with less than two minutes remaining in the 2nd or 4th periods. Team B may decline the penalty.  and have the ball placed at the previous spot, and there is no distance penalty.  But the timing rules still apply, and the game clock will start on the referee's signal.

Even if team B accepts the penalty the clock can still start on the ready, if there's less than one minute remaining and team B takes the runoff. This is the one really weird timing rule in NCAA where the game clock can run even before a free kick is made.