History
D&D started as a series of little booklets, now called "original D&D" (OD&D). These booklets were basically barely-edited versions of the house rules of Gary Gygax and Dave Arneson.
In 1977, TSR hired J. Eric Holmes to develop a Basic D&D game. This was a dark blue, boxed set containing D&D in a single book, plus a module (B1 In Search of the Unknown), and some dice (or cardboard chits, when they ran out!).
Moldvay and Mentzer are game designers who took the old Basic D&D game (edited by Eric Holmes) and revised them. Both produced "red box" versions of the game. You'll find far more differences between Holmes and the later red boxes than you'll find between Moldvay and Mentzer.
Tom Moldvay revised the "Basic" D&D game in 1981. It came in a red box and featured the B2 Keep on the Borderlands module. It came with dice (and a marking crayon!). These rules handled levels 1-3. David "Zeb" Cook wrote the follow-on "Expert" rule book (another boxed set) that expanded the game to levels 4-14.
Frank Mentzer revised the game again in 1983 with another "red box" set featuring the art of Larry Elmore. This time, the Dungeon Master book was separated from the Player book. Mentzer would continue the Basic (1-3) and Expert (4-14) classifications but would go on to produce additional expansions: Companion (15-25), Master (26-36), and Immortal (characters too sexy for their levels, but you essentially get 36 more). These separate books would later be combined into the D&D Rules Cyclopedia.
Differences between Holmes and Moldvay
Moldvay made many changes to the Holmes version to streamline play and make it easier for players to understand the game. Both games cover levels 1-3, though.
Overall differences:
Holmes' game includes B1 In Search of the Unknown. Moldvay's game includes B2 Keep on the Borderlands.
The Holmes version is intended as an introduction for Advanced Dungeons & Dragons, and refers the reader to there for further help. Moldvay Basic D&D is intended as its own game, with little connection to AD&D.
Holmes' book is a reference manual. Moldvay's book is an instruction manual.
Rules differences:
Holmes presents the game as rules to be followed. Moldvay presents the game as guidelines to be considered.
Holmes has initiative in order of dexterity (high to low). Moldvay has players roll group initiative.
Combat in Holmes is based on OD&D, which was based on Chainmail (more wargamey). The weapons all do 1d6 damage. Moldvay gives weapons individual damage ratings.
The spell Magic Missile requires a to-hit roll in Holmes, but not in Moldvay.
Holmes offers dozens of spells (level 1-3). Moldvay cuts this spell list a lot (from 18 to 3 3rd level spells, for instance).
In Holmes, not all ability scores have modifiers. Moldvay makes every ability count and provides bonus charts for each one, and most fall into the same seven bands (-3 to +3).
There are differences in advancement for classes. Elves in Holmes need far more XP to advance than in Moldvay.
Holmes has no surprise rules. Moldvay does, but they're essentially brought back in from OD&D.
Moldvay adds monster morale.
Moldvay adds automatic hits on a 20 and automatic misses on a 1.
Holmes carries forward the OD&D class name "Fighting Man." Moldvay shortened that to "Fighter" (probably copying Gygax in AD&D).
Differences between Moldvay and Mentzer
In general, the Mentzer version was a repackaging and expansion of the Moldvay version. The differences are minor in the Basic ruleset.
Overall differences:
Moldvay aims his writing at a younger audience. Mentzer writes for an adult audience.
The Moldvay version has weaker layout and art than the later Mentzer version.
Moldvay's game is pretty simple and straightforward. Mentzer adds complexity, like skills and weapon mastery.
Moldvay's red box came with B2 Keep on the Borderlands, but you could buy the books separately (unboxed). Mentzer's Basic box didn't come with a module (the Expert set came with X1 The Isle of Dread, though!).
Rule differences:
Moldvay stops at level 3 (and Cook's Expert set continues that to 14). Mentzer's "BECMI" continues on and on.
Moldvay states that clerics get their spells from gods. Mentzer gets all "wishy-washy"* about this aspect of the game and only says clerics get spells from "their beliefs."
Moldvay's magic-users get one spell at 1st level and have to find more in play. Mentzer's get one spell plus Read Magic at 1st level, and then one new one at every level.
The monster list changes between these versions. A number of people "monsters" are combined into the Human entry: acolyte, medium, trader, veteran. Insect swarm and noble are moved to the Expert rules. Some monsters are renamed: cave locust became locust, giant; driver ant became ant, giant; and killer bee became bee, giant.
Mentzer slows down the advancement of saving throws, thieves' abilities, and spell acquisition for clerics and magic-users.
Castle-building rules are more detailed in Moldvay, but Mentzer details a base town and talks about running town adventures.
Best Answer
The Challenger Series more of a generic category for products designed for use with the Rules Cyclopedia. My guess is that the reason for the terminology is because the books were an alternative/supplement to the Entry Level products that were used with the boxed D&D beginner's set. [source]
I believe this to be a comprehensive list of all Challenger Series products:
The adventure modules take place in the Mystara campaign setting.
As for The Night Howlers, it looks like it's the fourth in a series of Creature Crucible books. The crucibles detail the society/background of non-typical character races, and provide rules for playing them. I'm not entirely sure why it's not in the lists of Challenger Series products I found.