On +1 swords: it is only "just another +1 sword" if you let it be. Every edition of the game has, in supplements and Dragon and the like, offered, somewhere, lists of ways to make those +1 swords unique (and not necessarily by adding powers, either). there's a reason for this. A "+1 sword" is dull and uninspiring. Gregor's Blade, used by the legendary troll-hunter to cut the arm from the Darkling Prince at the foot of the Chaos Gate, is interesting, and quite frankly, the number of "plusses" on it doesn't matter one whit. When the player character who found it swings it in desperation at the spectral thing trying to devour his essence, and the thing actually screeches and flees, that character is going to recognize the power of that weapon and isn't likely to kick it to the curb when the "+2 sword" pops up in Unnamed Dungeon #5. Want to make +1 swords interesting? Get rid of plusses entirely.
On spells and magic: The list of spells in the PHB is the list of spells common and available to player character casters. It does not represent the whole of spell knowledge in the world, or represent spells that non adventuring spellcaster types even have access to. Local wise men and women will have their own spell lists, designed to ease birth and help crops grow and read the flights of birds. The vizier's of decadent emperors will have their own spell lists, designed to inspire fear and awe in the populace, provide pleasure and health to their masters, and allow themselves to gain more and more power behind the throne. Necromancers, demonologists and fleshweavers should all have like lists: unique spells geared toward what they use magic for. Don't have time to create lists of new spells? thankfully, there's tons and tons of spells out there in supplements, 3rd party products and magazines to choose from. Just don't let the PC casters have access to them (unless, of course, they want to delve into those other arts, for which there will be a price to pay...).
On monsters: Why have ten manticore when you can have just one, The Manticore. As with spells, there are literally tens of thousands of monsters to choose from out there. Making The Medusa, The Minotaur or The Dragonne a unique creature will not make the DM want for creatures. Or, simply change the description -- or presentation of the description -- of the monster. You may know that those creatures with skin of stone and great crushing boulders for hands are trolls, but your players don't have to. Or do the flip side: an ogre isn't an ogre when it is a creature with the lower body of a bull and the upper body of a minotaur.
The point is that with players familiar with the tropes of D&D, the key to getting their attention and bringing the mystery and magic back is to break, twist or alter their expectations. In addition, as DM you have the right and responsibility to just make crap up that will entertain your players and make for a better game. Pulling the same old stuff out of the monster manual, going by the letter of the rules all the time, and just plain doing things by the book is simplistic, bottom floor DMing.