My personal favorite entry is this one from September 12 as it contains one of my favorite pieces of communication that President Lincoln ever sent. I will copy and paste this response below, but will not copy the whole correspondence between Lincoln and Union officials in Kentucky as you can see that on Allen's site. (I added the emphasis in bold.)
Major-General BOYLE, Louisville, KY:
This response always fascinates me, especially when the President openly admits he respects General Horatio Wright's opinion more than General Jeremiah Boyle's. That's a pretty blunt and frank statement, especially from a man often considered to be very diplomatic and patient with many of his troops (especially this early in the war.) Perhaps this is a reflection of Lincoln's stress level, considering with the Confederates invasion of Maryland (being defended by General George McClellan, in whom Lincoln did much have much faith), this apparent invasion of Kentucky with such demands coming from Boyle and others, and Lincoln's waiting for an opportunity to introduce the preliminary Emancipation Proclamation, which he knew would be a huge announcement once he found the right time. The late summer and fall of 1862 was a very difficult time of the war for Lincoln and this response may be a sign of that.
Boyle's response is interesting too, beginning with the admission he did not expect the Confederates to be near Louisville soon and then stating he did not believe Bragg had a large force in the state.
All-in-all, this small exchange shows Lincoln taking charge of the situation, expressing his honest feelings in trying to determine if the situation was truly serious or was simply an over-reaction by Union leaders in the area. This was just one of the worries Lincoln had at the time, but if it was not truly as bad as he had been told, it was a waste of his time. Eventually, the situation did become quite serious with Bragg (and Kirby Smith) having troops in the state that Lincoln so badly wanted to keep in the Union, leading to the Battle of Perryville, one of the most severe fights in the western theater of the war.