I suggest Illustrator. With its diagramm tools you can create any kind of diagram and its fully editable. Also you can output any kind of format in any resolution since its verctorbased graphics.
Of course, illustrator isn't free. If you don't want to invest money, maybe there's an alternative for you here.
I don't know whether those are suitable for you. If you "draw" your diagrams, also Photoshop can be useful.
I am not familiar with the pencil/dia tool" you are using, but might it be, that its not the software? Maybe you can change any kind of export options like quality, resolution or text-rendering? If you're using Photoshop, check what kind of text sharpening you got activated. For web (what i assume you're working for, since you export .png's) i'd recommend "sharp" mode. you find the option in the top option-bar.(sry my PS is german, but i guess it looks the same in english)