PZ Myers has a stab at encompassing the deep time of hominid evolution in his recent post The proper reverence due to those who have gone before.
HP Lovecraft seemed to be transfixed by a fear of vastness, and transmits this awe in his books: "Life is a hideous thing, and from the background behind what we know of it peer daemoniacal hints of truth which make it sometimes a thousandfold more hideous. Science, already oppressive with its shocking revelations, will perhaps be the ultimate exterminator of our human species -- if separate species we be -- for its reserve of unguessed horrors could never be borne by mortal brains if loosed upon the world." Here are some more juicy quotes.
Vernor Vinge, I think, does a good job of conveying the size of space and time. Are there others you would recommend?