First of all great thread.
1) Dragons - I agree with the sentiment about dragons thus far. Keep them rare and special. That being said an adventure line with lots of kobold minions leading up to a dragon would be cool too. But please do not overdo what I feel is the most iconic of adversaries.
2) Goblins - Goblins are fun little monsters for a low level encounter. If used properly, set up and established with the care of a pc almost then a simple goblin band becomes memorable. Placing 3 or 4 goblins in the woods to attack the pc's when the sleep makes the goblins cannon fodder. Make the pc's attack a well thought out and trap laden lair with guard dogs and sentries makes them mean little buggers.
3) Orcs - Another race that suffers from poor planning. Make them as vicious and brutal as they are and don't pull punches with them. They are the usual next step up from goblins and kobolds.
4) Drow – To start off, I am completely against good drow. They are an evil race and should remain so like the vampire should ALWAYS be evil. A well thought out devious and sadistic plan by a drow matriarch can be a beautiful thing to GM. That being said drow have their place and should not be over used. They are like a high class dessert that should be savored. Besides most drow only show themselves when they have the advantage and the pc’s don’t not the other way around.
5) Dinosaurs - I never saw a place for dinosaurs in a fantasy setting personally. How many legends have a knight on a steed tilting against a stegosaurus?
6) Undead - I agree undead are overused but only mindless undead. Bring on the liches, ghosts, vampires (please to all that is holy the NON-sparkly kind), and other intelligent undead. Undead can be a great role play opportunity especially with ghost as you need to find out what is needed to put them to rest. Unintelligent undead is just another blender situation. Put them in and let the swords dice them up. Some players like to do mindless hack and slash and mindless undead is a good opponent for them. I use a good number of intelligent undead and outsiders in my home brew games because I value the pc's thinking of alternative ways to get through encounters.
7) Swarms - Annoying at best. Deadly at worse.
8) Outsiders - Ah outsiders a personal favorite. I adore devils and demons and the role play opportunity they afford. Nothing like trying to corrupt the party or get them to make a deal for the greater good with an evil outsider that will always come back to haunt them at the worst possible moment.
9) Humanoid NPCs – This is always going to be the most used boss type. It is the most varied and the easiest to stat up. Also most of the interactions on a meaningful level will be with the creatures pc’s see as equals and humanoids are the way to go for the emotional attachment that most players are looking for. It is hard, not impossible; to hate a winter wolf. However a den of thieves is much easier to form an emotional antipathy towards. Also in this category is this most common reoccurring villain. You can have an undead or an outsider as a reoccurring villain but the humanoid usually makes the most sense. They have the widest level range and you are not roped into having the CR set by the type of creature. So setting a human rogue or evil ranger or wizard up as a reoccurring villain at 2nd or 3rd level can be easily done. Great potential here to be exploited keep using them as much as possible and give them gear like pc’s and pc like abilities and have their strategies use them effectively.