Sorry gang, this is just how my head works... I love lists!  So here's a list of all the ongoing Archie characters, secondary characters, family relations, etc. Please feel free to add to this as it is constantly being updated!

Archie Andrews; Betty Cooper; Veronica Lodge; Jughead Jones; Reggie Mantle;

Jughead Jones [Forsythe Pendleton Jones III];

Cheryl Blossom; Jason Blossom; Sharon Blossom (Cheryl's Scottish Ancestors from Cheryl Blossom # 31)

Dilton Doiley; Danni (Dilton's girlfriend from the Strange Science books)

Nancy Woods (also called Harris); Chuck Clayton;

Moose Mason  [Malcolm]; Midge Klump; Ethel Muggs;

Bridgette Reilly; Ginger Lopez; Tomoko; "Plain" Jane Parker; Maria Rodrigeuz; Frankie Valdez; Zelda Twurl; Twula Twist; Cricket O'Dell; Wendy Weatherbee; Jinx Malloy:

Pop Tate; Segarini (a rival of Pop's)

(the Andrews family)

Fred Andrews; Mary Andrews; Grandpa Andrews (Archie #500 and few other issues); Aubrey Andrews (Archie's Scottish Ancestors from Cheryl Blossom # 31)

(The Lodge Family)

Hiram Lodge; Hermoine Lodge; Smithers; Gaston (the cook); Fifi (the maid); Ms. Snodgrass (Mr. Lodge's secretary); Oscar (a dog); Fifi (Veronica's dog, a poodle); Frou Frou (another poodle);

(The Cooper family)

Hal Cooper; Alice Cooper; Caramel (Betty's cat); Polly Cooper (sister); Chic Cooper (brother); Lydia Wyndham; DeClan McManus;

(The Jones family)

Forsythe P. Jones II [Forsythe Pendleton Jones II]; Gladys Jones; Jellybean [Forsythia]; Hot Dog; January McAndrews (Jug's girlfriend from the Time Police books); Colonel Pickens (Jughead's Ancestor from Jughead's Time Police & Archie's Weird Mysteries)

(The Wilkin Family)

Bingo Wilkin (Jughead's cousin)
Willie Wilkin (father)
Wilma Wilkin (mother)
Uncle Herman
Rebel (the dog)

(The Smythe Faimly)

Sampson Smythe
Shiela Smythe
Samantha Smythe

There's also Bingo's band members, Terrible Teddy and Buddy

(Faculty at Riverdale High)

Waldo Weatherbee (principal)
Geraldine Grundy (English)
Professor Benjamin Flutesnoot (the school science teacher)
Bernice Beazly (the school cook) (also spelled Beazley/Beasly/Beasley)
Ms. Ophelia Hammly (drama class)
Mr. Svenson (janitor)
Ms. Phlips (the Bee's secretary)
Coach Kleats
Coach Floyd Clayton (also called Harry)
Miss Simkins (math)
Superintendant Hassle
Miss Haggly (history)
Mr. Grimley (a guidance counselor)
Miss Harriet Burble (a guidance counselor-- also called Mrs.)
Patton Howizter (Vice-Principal)
Michael Dee (librarian, media specialist)
Raul Flores (mathematics and computer science)
Greta Grappler (girls' physical education)
Putnam Grimley (drivers education)
Hiram Gaffer (crossing guard)
Wanda Wheeler (bus driver)

Katy Keene; Mackenzie Keene (was Melissa);

Sabrina Spellman; Salem; Aunt Hilda; Aunt Zelda; Ambrose; Della, the head witch; Harvey Kinkle;

(pre-teen Sabrina series): Gem Stone, (Sabrina's nemesis), Llandra; Chloe

(anime Sabrina) Shinji

Josie and the Pussycats [Josie McCoy; Valerie Brown; Melody Valentine]; Alexander Cabot III; Alexandra Cabot; Alan M. Mayberry; Alexander Cabot II (Alex and Zan's father); Valerie Brown was Valerie Smith as late as 1988

Madelyne (Veronica's cousin); Marcy (Veronica's cousin);  Leroy (Veronica's cousin); Amber and Tyler (Betty's cousins); Aunt Clara (Veronica's aunt, Hiram's sister); Souphead Jones (Jughead's cousin)

The Veronicas (Jess, Lisa);

Jingles; Sugar Plum

Li'l Jinx; Greg; Fat Charley Hawse; Russ; Gigi; Hap and Merry Holliday (Li'l Jinx's parents); Roz (Russ' female friend) and Mort the Worry-Wart

(specific Little Archie characters)

Fangs Fogerty and his Seaside Serpents gang, Mad Dr. Doom, Doom's boy sidekick (Slick?), Sue Stringley (the poor girl from the wrong side of the tracks), Evelyn Evernever (who had a lookalike doll named Minerva)

(New Archies characters)

Eugene; Amani

The Archies [Archie Andrews; Veronica Lodge; Betty Cooper; Reggie Mantle; Jughead Jones];

Pureheart the Powerful [Archie Andrews]; Evilheart [Reggie Mantle]; Superteen [Betty Cooper]; Captain Hero [Jughead Jones]

The Man From R.I.V.E.R.D.A.L.E. (Really Impressive Vast Enterprise for Routing Dangerous Adversaries, Louts, Etc.);
A.R.C.H.I.E. [Archie Andrews]
V.E.R.O.N.I.C.A. [Veronica Lodge]
B.E.T.T.Y. [Betty Cooper]
J.U.G.H.E.A.D. [Jughead Jones]
R.E.G.G.I.E. [Reggie Mantle]
P.O.P. [Protect Our Planet]

C.R.U.S.H.; Dr. Demon; Dr. Nose; Li'l Devill; Mr.X

Explorers of the Unknown [Red [Archie Andrews]; Angel [Veronica Lodge]; Nitro [Reggie Mantle]; Squint [Jughead Jones]; Wheels [Betty Cooper]; Gizmo [Dilton Doiley]; Spike [Moose Mason]; F/X [Chuck Clayton]]; Blaze [Cheryl Blossom]

Archie1 (Archie characters as cavemen)

I admit that the cast of the Wilkin Boy isn't here, but I haven't read  any of those books. I'm especially looking for creative acronyms for the R.I.V.E.R.D.A.L.E. characters' names... 

Any and all additions appreciated (nothing like a little alliteration to start the morning...)

Gregg

Added all the suggestions listed by the other members. Thanks people! 

Actually, I should also mention that in the '70's and '80's revivals of Katy Keene, her younger sister was also called Melissa.

An addition to the "Jones Family" section:

Souphead Jones (Jughead's younger cousin) - doesn't show up much

According to a story in the latest issue of Jughead and Friends, Mrs. Smythe's name is Sheila. Also, it's "Sampson", not "Samson".

Lydia Wyndham; DeClan McManus;

Who are these?

Miss Harriet Burble (a guidance counselor) also called Mrs.
Patton Howizter (Vice-Principal)

Is something missing?

Explorers of the Unknown [Red [Archie Andrews]; Angel [Veronica Lodge]; Nitro [Reggie Mantle]; Squint [Jughead Jones]; Wheels [Betty Cooper]; Gizmo [Dilton Doiley]; Spike [Moose Mason]; F/X [Chuck Clayton]]; Blaze [Cheryl Blossom]

I'm kind of interested in what this series is like, if someone's willing to start a thread for it elsewhere.

2 characters that showed up in Betty's Diary: Lydia was a mystery writer that Betty befriends. DeClan is her love from years past.

Wow, I'd completely forgotten about Lydia and DeClan. Those were really good stories and another example of good Archie stories that don't follow the mold.

I see you have Ambrose, but are missing Fangs Fogerty, his Seaside Serpents gang (I think that was their name), Mad Dr.Doom, Doom's boy sidekick (Slick?), the poor girl from the wrong side of the tracks. Sorry for not having the names!

I think I can help out with that.  If memory serves me, the poor girl in the Little Archie stories was named Sue Stringley.

There was actually a couple of stories that featured Archie and the gang meeting up with three former Little Archie characters.  There was one story where Archie and the gang threw a party for Ambrose, there was one where Archie and the gang meet up with Sue Stringley, who is now a high-end model! (go figure), and there's one where Archie is reunited with Freddy "Fangs" Fogarty.

I can't recall the exact issues these stories are found in...if I come across them, I will definitely update you on them.  But, I am sure of one story.  The Fangs/Archie reunion can be found in the beginning of Archie's Double Digest #117, which was released in 2000.

Captain Hero - you are bringing back fond memories to me with Mort the Worry Wart and Roz! I miss Lil Jinx. I don't know why Archie Comics stopped reprinting these in the regular comics. I never read the one with Fangs. I'm going to have to hunt down that Digest now!

The New Archies could be the only variation of Archie that I didn't really like. Not for omissions of characters but their attempt to be hip (at the time) was so painful!