This all depends on your particular campaign, I think. Keep that in mind as you apply these guidelines.
4E gives each creature an origin.
- Common: natural, spirit
- Uncommon: elemental, fey, shadow
- Rare: aberrant, immortal
My mental rules for categorizing origins is based on "distance" from the characters' world:
- Natural is everyday for heroic-tier characters. Spirit belongs in the regular world.
- Elemental, fey, and shadow creatures are from other "nearby" planes, so they're uncommon, but not unheard of.
- Aberrant creatures are often from the Far Realm. Immortal creatures are often from the Outer Planes. Thus, these are very rare.
4E gives each creature a type.
- Common: humanoid, beast
- Uncommon: magical beast
- Rare: animate
My mental rules are sort of arbitrary here, but you can see how I'm thinking.
4E describes each creature with any number of keywords.
Common: blind, bugbear, cold, dragonborn, drow, dwarf, earth, eladrin, elf, fear, fire, force, gaze, genasi, giant, gnoll, gnome, goblin, goliath, half-elf, halfling, healing, hobgoblin, human, illusion, implement, inspired, kobold, lightning, living construct, lizardfolk, mount, necrotic, ogre, ooze, plant, poison, psychic, radiant, reptile, shifter, sleep, spider, swarm, thunder, tiefling, troll, undead, warforged, water, weapon, zone
Uncommon: air, aquatic, change shape, construct, doppelganger, dryad, grimlock, hag, homonculus, hydra, magebred, minotaur, oni mage, rakshasa, roc, sahuagin, shapechanger, slaad, sphynx, vampire, wight
Rare: angel, dark one, demon, deva, devil, dragon, exalted, girallon, githyanki, githzerai, ice archon, phane, primordial, shulassakar, shunned, spellscarred, yuan-ti
My mental rules for categorizing keywords:
- If the keyword is a PC race (dwarf, tiefling, warforged), it's common.
- If the keyword is an effect type (blind, illusion, weapon), it's common. Except for certain effects that heroic-tier characters rarely can handle (air, aquatic).
- If the keyword is a generic creature type that heroic-tier characters encounter often (goblin), it's common; specific creature type keywords (vampire) get bumped up to uncommon. Really weird creature types get pushed to rare.
- If the keyword is a creature type from the Far Realms or Outer Planes (angel, githyanki) or is immortal (exalted, primordial), it's rare.
- Judgment in between.
You can look at other creature characteristics for determining rarity.
Vision: a creature with darkvision is probably uncommon and a creature with truesight is probably rare.
Role: minions, soldiers, and skirmishers are probably common; artillery and brutes are probably uncommon; controllers and lurkers are probably rare. Same for Group Role: standard and minion are common; conjured and elite are uncommon; solo are rare.
There are many ways to divide creatures into common, uncommon, and rare types, but the most important guideline is to do what is right for your game setting. What kinds of creatures do you want PCs to encounter most often? What kinds of creatures are "special treats" that show up very rarely?
So now you've decided what is rare and what is common. How do you manage this?
Make a list of common monsters. You don't need to make an exhaustive list. Just pick 10-20 that appear often in your campaign. Make another, shorter list of 3-5 uncommon monsters that you might want to use some time. Don't worry about rare monsters. Just pick them when you need one.
Random encounter tables. A good way to turn your decisions into something with mechanical weight is to create random encounter tables for different environments (forest, dungeon, urban, sewers, long roads, etc.). Make a 3d6 table for each one with the following bands, and then fill in some monsters. When you need a random encounter, roll and trust the dice.
3D6 ROLL IN 216 PROBABILITY RARITY
3-4 4 2% rare
5-6 6 3% uncommon
7 10 5% uncommon
8 21 10% common
9 25 12% common
10 27 13% common
11 27 13% common
12 25 12% common
13-14 31 14% common
15-17 9 4% uncommon
18 1 <1% very rare
Annotate your monster manuals. Sacrilege, right? You can buy some sheets of those adhesive "dots" in three different colors (I suggest green, yellow, and red for common, uncommon, and rare) and go through your books and put a dot next to each creature listing to indicate rarity. Of course, if you change your mind or start a new campaign with different goals, you will have to figure out how to get the dots off...
Make exhaustive lists. If you're a real masochist, find a list of all the creatures from the sources you use, and import them into a spreadsheet and add a "rarity" column and start categorizing...