If you are at the part right after the parking office where a huge bus is and you have over 2 minutes or more, mutated Nemesis will appear. Kill him and you will get a 120 second time bonus.
To get Jill's Diary, you'll need to get all of the files in order. After getting the last file, you will see that Jill's Diary will replace Operation Instructions A.
Each time you defeat Nemesis in Hard Mode he will drop something.
Near the end of the game where you have to beat Nemesis with the rail canon, look at the huge body near one of the batteries. This is Mr. X form Resident Evil 2.
After you unlock all of the character endings, you will see a special message from the director. One word of caution, this will be the only time you can see this.