Quote 1
The impression I had was that we were leaving the West and entering the East. (1.1)
Harker considers Budapest, the capital of Hungary, to be the last outpost of "the West" as he enters "the East." It's a total cultural change after crossing the river—in the "East," everyone is superstitious and caught up in traditions. Also, there are vampires.
Quote 2
This was the being I was helping to transfer to London, where, perhaps, for centuries to come he might, amongst its teeming millions, satiate his lust for blood, and create a new and ever-widening circle of semi-demons to batten on the helpless. The very thought drove me mad. (4.62)
Jonathan imagines Dracula invading England and glutting himself on the blood of English people. He feels powerless to stop him, and imagines that the English will be likewise "helpless" against the vampire.
Quote 3
There was something about them that made me uneasy, some longing and at the same time some deadly fear. I felt in my heart a wicked, burning desire that they would kiss me with those red lips. It is not good to note this down, lest some day it should meet Mina's eyes and cause her pain; but it is the truth. (3.29)
Jonathan's repressed sexual desire comes bubbling to the surface when he sees the sexy vampire ladies in Castle Dracula. He's both attracted to them and repulsed by them, and ashamed to admit that he kind of wants them to kiss him.
Quote 4
"You know, dear, my ideas of the trust between husband and wife: there should be no secret, no concealment." (9.2)
This is Jonathan Harker's ideal of marriage. Of course, he's the one who breaks this ideal when he stops keeping Mina in the loop about their fight against Dracula. And look what happens! She gets bitten.
Quote 5
There are many odd things to put down, and, lest who reads them may fancy that I dined too well before I left Bistritz, let me put down my dinner exactly. I dined on what they call "robber steak" […] The wine was Golden Mediasch, which produces a queer sting on the tongue, which is, however, not disagreeable. I had only a couple of glasses of this, and nothing else. (1.17)
Jonathan Harker assures any future readers of his diary that he wasn't drunk the night he traveled to Castle Dracula. He anticipates that some people might assume that he was hallucinating or in an alcohol-induced haze when they read about the "blue lights" and the wolves, so he tells us exactly what he had to eat and drink beforehand.
Quote 6
[…] I fell to at once on an excellent roast chicken. This, with some cheese and a salad and a bottle of old Tokay, of which I had two glasses, was my supper. (2.18)
Again, Harker is careful to tell us exactly what he had to eat and drink—maybe he's anticipating, again, that future readers of his diary might assume that he was hallucinating the strange things he witnessed at Castle Dracula.
Quote 7
[…] there was that in his eyes and in his bearing which made me remember that I was a prisoner, and that if I wished it I could have no choice. The Count saw his victory in my bow, and his mastery in the trouble of my face […] (3.15)
Jonathan is powerless in Castle Dracula. Look at the language he uses! He knows that the Count has "master[ed]" him.
Quote 8
I closed my eyes in a languorous ecstasy and waited—waited with beating heart. (3.32)
Even as he's about to be kissed/bitten by the sexy vampire, Jonathan remains passive and still.
Quote 9
The sight seemed to paralyse me […] (4.62)
The very sight of Dracula's face, even as he's sleeping (or whatever it is vampires do), is enough to "paralyse" Jonathan.
Quote 10
I am alone in the castle with those awful women. Faugh! Mina is a woman, and there is nought in common. They are devils of the Pit! (4.67)
Here, Harker contrasts the three Brides of Dracula with Mina. We're invited to think of them as the complete opposite of Mina.
Quote 11
At least God's mercy is better than that of these monsters, and the precipice is steep and high. At its foot a man may sleep—as a man. (4.70)
It's interesting that Jonathan adds "—as a man" at the end, because at this point, he has no way of knowing that the vampires' kiss could turn him into a vampire. All he knows is that "those awful women" want to suck his blood and that Dracula, too, is some kind of monster. Maybe Harker thinks that being victimized by the three "weird sisters" would somehow make him less of a man.
Quote 12
But my very feelings changed to repulsion and terror when I saw the whole man slowly emerge from the window, and begin to crawl down the castle wall over that dreadful abyss, face down, with his cloak spreading out around him like great wings. (3.22)
This is one of the first hints Jonathan has that the Count isn't quite… human.
Quote 13
What manner of man is this, or what manner of creature is it in the semblance of a man? (3.23)
Jonathan might not know what, exactly, Dracula is, but it doesn't really matter. The fight against evil is on!