
I warn you now, THERE ARE SPOILERS WITHIN THIS THREAD. If you have not seen the latest episode, turn away NOW before you clutch the sides of your head and scream "NOOOOOOOOOOOO! RAZOR! WHY DID YOU SPOILERISE ME!?!?! NYARRRRGHHHHH!!!" And proceed to throw a brick wrapped up in a flaming frozen waffle at me.
Also contains useful / interesting info on episodes already aired when and as I come across such information. If you find something, post it here!
SPOILERS BEGIN HERE. YOU HAVE BEEN WARNED.
Also, Cake.
Upcoming Epsisode List (After "Along Came a Spider")
Note: Brackets are my thoughts

Sound and Fury
Lost and Found
Survival Of the Fittest
Headmaster (!?!)
Nature Calls (Call of the wild reference?)
Megatron Rising Part 1 & 2
The Elite Guard
Return of the Headmaster (looks like we're getting a continuity here, and not a series of individual plots!)
Mission Accomplished
Garbage in, Garbage out
Velocity
Rise of the Constructicons (!?!)
A Fistful of Energon
S.U.V.: Society of Ultimate Villainy
Autoboot Camp
Black Friday
Sari, No Ones Home
A Bridge too Close Parts 1 & 2
Characters not yet introduced (As of Along Came a Spider)
Wreck Gar
To Be voiced by Weird Al Yankovic!
To Appear in the following
Sound And Fury
Black Friday
Mission Accomplished
Return of the Headmaster
Nature Calls
Blurr
Sound And Fury
Black Friday
Mission Accomplished
A Fistful of Energon
Megatron Rising Part Two
Jazz
Sound And Fury
Black Friday
Mission Accomplished
Return of the Headmaster
S.U.V.: Society of Ultimate Villainy
Arcee
Voiced by Susan Blu!
Sound And Fury
Black Friday
Mission Accomplished
A Fistful of Energon
Sentinel Prime
Sound And Fury
Black Friday
Mission Accomplished
Return of the Headmaster
Known References to Other TF Series
Transform and Roll Out Parts 1 - 3
The opening scene of episode one - Transform and Roll Out - is a direct reference to G1 with footage taken directly from G1's MTMTE Part 1 and used as "Historical Footage". The last scene from the historical archive appears to be wheelie (unsure).
Optimus can close his face plate in a similar manner to Optimus Primal from BW and Optimus Prime from the Movie.
The decepticon warship seen in episode one appears to have the same hull design as The Nemesis from Beast Wars.
Blackarachnia seems to be wearing the same helmet in Animated as she does in BW.
When being attacked by the Decepticons, Bumblebee says "We're all gonna die, aren't we?". Might be a little Rattrap in there as well

The firing sound of Megatrons Cannon is similar to G1 Megatrons Cannon.
Sari's Dog is named "Sparkplug", a reference to G1.
The scanner launched when Optimus and the crew re-awaken is the same as the scanner used in G1 to scan for local life forms.
The scanning effect used is also the same.
The Transformation sound is from G1.
Theres a scene where Optimus and Starscream are fighting and crash through a building, possible a reference to the Movie where Prime and Megatron are fighting and crash through a building.
Upon Optimus death, he turns Grey like his original movie counterpart. As usual, he gets resurrected.
Sparks seem to have a similar visual to Beast Wars Sparks.
Sumdak's technological mastery is apparently due to reverse engineering tech cannibilised from Megatrons head, a reference to the recent movie where all modern technology is derived from Megatron.
Home is where the Spark is
"If the titanium alloy plating fits, wear it! And... I make it look good!" - A MIB Reference
Megatron's usage of the "Pocket Bots" is very similar to Beast Machines Megatron when he wrought havoc from within the body of a diagnostic drone.
Total Meltdown
Bumblebee leaks a purplish fluid when he gets damaged; Mech Fluid?
At approximately 12:01, a Sumdak robot breaks down. The sound appears to be the same as that of a Zat'naka'tel from Stargate SG1
Ratchet mentions sound frequencies disrupting techno organic circuitry
Blast from the Past
Dinobots. Do I honestly need to say more?

Bulkheads training ground and subsequent home of the dinobots is reminiscent of Dinobot Island.
Thrill of the Hunt
Lots of scenes from the Great War
Arcee's first appearance!
"Ow! Not the racing stripes!" reference to Bumblebee's racing stripes from the recent movie.
When prowl rips off a laser cannon and starts firing it, the sound is identical to Cheetors "Gut Gun".
Along Came a Spider
Elita One (G1)
Sentinel (Unsure)
Blackarachnia!
~5:35 into the episode, when Sentinel cuts the webbing trapping Elita with his shield, the sound of a Zat from SG-1 is heard again.
When Optimus walks into the decepticon ship after being separated from Elita, he encounters a hold full of Energon cubes which appear exactly as they do in G1.
~9:48 In the lower left corner of the screen, BW Blackarachnias helmet can be seen. Look Below for Piccy Goodness!

Blacharachnia's beastmode appears to derive mainly from it's Transmetal 2 incarnation in Beast wars. Her robot mode appears to derive from her BW Original, BW TM2, and BM Technorganic mode.
She also has the "Hourglass" marking on her abdomen, hips and forehead.
Mention of Organic components masking energy signatures (BM)
Of Note; The stuffed Spider in the park in the initial and second last scene has the Blackarachnia's hourglass symbol on it's abdomen.
Thoughts and Opinions thus far:
Bumblebee appears to be a synergy of Bumblebee from G1 and Cheetor from Beast Wars with his speed demon traits and general "Offical Team Noob" role

Ratchet seems to be a synergy of Rhinox in a bad mood an Kup on his more senile days.
Optimus speech in the first episode is practically the "Destiny and Honor" speech that Megatron from BW derided Optimus Primal for. When I made that connection, I couldnt help chuckling all the way through it.
Starscreams acting ability is phenomenal. Openly traitorous in the prescence of everyone except for Megatron. The moment he crosses into frame, he immediately plays the part of sniveling sycophant with gusto.
Megatrons character and voice is very well done. I'd vote him as Harbinger of the apocalypse any day.
Sari's "What's it like to go to school with other kids" comment sounds like she's being overly sheltered by her dad.
Sari's character seems to be a refreshing break from the traditional role of having a young adolescent male as the Transformers main human contact.
"This is why I hate Machines" - This repeated line only gets better and better every time I hear it.
Prowl's battle "Facemask" completes his ninja look wonderfully.
When Sari whispers the "secret" of how organic life propagates, the look on his face is priceless!
When the Allspark scans Sari, there are several images that flash across the screen.
The images are as follows:
Images flowing FROM the allspark are
Ultra Magnus
Optimus Prime
Megatron
Starscream
Optimus Prime (Cybertronian Vehicle Mode)
Ratchet (Vehicle Mode)
The Allspark
The Autobot Shuttle
Images flowing FROM Sari are
An unknown man dressed in a suit
An unknown woman dressed in a suit
A Pudgy male child
Earth
The Pyramids
Flowers
A Horse
Waves on an Ocean? (Image Below!)

Bacteria
A DNA Molecule
Prowl's apparent fascination with organic life is a nice touch and will be interesting to see how this develops as things roll on.
Ratchets character development and historical background in Thrill of the hunt, not to mention the episode as a whole, is utterly phenomenal and involves some top class writing and consideration on part of the creators. The result is an emotionally charged action packed episode that pulls at the heart and doesnt get boring. As far as episodes go, you cant get much better than that.
Great Lines from Nanosec
"Denied!"
"Definitely lose the suit, it makes you look 10 years older!"
"...That is faaaaaaaast!"
"I suspect it was an inside job"
In Nanosec, the savings account number of Issac Sumdak is
0000 2328 7401
However, at the ATM, the number Nanosec punches in is
0900 2328 7401
Which appears to be an animation goof.
The second number may reference a phone number. (?)
There seems to be an implied relationship between Elita and Sentinel in the flashbacks Optimus has. In the first flashback, Sentinel has his arm over Elita's shoulder.
This contrasts however with Prime's treatment of Elita/Blackarachnia later in the episode. How Sentinel, Prime and Elita's relationships linked up has yet to be seen.
Sentinel also seems to be a robotic version of Captain America.
In addition, the spiders from "Along Came a Spider" have only 5 eyes.
"Give me one good reason why we should leave." **3 spiders drop down** "...How about three?"
When Blackarachnia steps up to Bulkhead, his jaw literally drops off. I lol'd.
Along Came a Spider is another phenomenal episode that delves into Optimus' Character whilst also introducing a new one. Elita One evolving into Blackarachnia was a very unexpected twist, one that I have to admit I'm liking more and more the more I think about it. The final scene definitely pulls on the heartstrings. Definitely a top episode, right up there with Thrill of the Hunt.
Sources:
http://imdb.com/title/tt1055335/episodes#season-1
Diligent watching of the series so far

Will be working on those screenshots once I've made this post.