Threads are always more awesome with pictures! (Okay, maybe not
always... I suppose a thread about feces or rotting flesh or something could do without photos... But I digress...)
Where was I? Ah yes... First off, a bit of a disclaimer. I am always hesitant to bring up third party figures in a thread outside of the third party forum... but you yourself acknowledged that such things may be necessary to fill some of the gaps Has/Tak haven't filled themselves yet. So I hope the more hardline anti-third party folk will forgive a touch of it.
Anyway, on with my post!
I'm going to present some photos, and below each photo will be a list of the figures in it. The list will be based on the vehicle modes in the photos, from left to right, back row to front row. After the character's name, it will state within parenthesis who the manufacturer is if it is a third party figure, or what figure it is if it is a repurposed figure (unless it is repurposed from a figure with the same name.) Some official figures may have third party accessories. These will only be noted if they make up a significant percentage of the whole. Also, many figures have Reprolabels, which will not be noted.
Any talk of repurposing is, of course, highly open to personal opinion and thus anything I say on the matter should not be taken as fact.
The TFWiki doesn't really have a list of which characters appear in which season. (Unless I missed something somewhere.) If you really want to know that, I suppose you'd have to look at the character listings for each episode and collate the data yourself. The closest the TFWiki does have is a list of which toys were released in the toyline each year, which is a close but not exact approximation.
I have my collection split up along similar lines. I have my "Season One" shelves, which are mostly those robots known to have been on the Arc when it crashed. (There are a few additional figures above that included, mainly as far as Decepticon jets are concerned.)
They are as follows:
Autobots:

-Hauler (repurposed from RTS Solar Storm Grappel)
-Prawl
-Ironside
-Gears (iGear)
-Trailbreakr
-Ratchet
-Optimus Prime (cab is Has/Tak, trailer is Fansproject)
-Huffer (iGear)
-Hound
-Sideswipe
-Bluestreak
-Wheeljack
-Sunstreaker
-Jazz
-Windchargr
-Brawn
-Bumblebee
-Mirage
-Cliffjumper
-Spike & Sparkplug (Impossible Toys)
Decepticons:

(Naming will be a bit tricky here, as the figures are less in even rows. Hopefully the list will be followable.)
-Purple Generics (x3) (CHMS)
-Reflector (Perfect Effects)*
-Megatron
-Acid Rain and other two Rainmakers (CHMS)**
-Sunstorm
-Soundwave
-Generic Black Seeker (CHMS)
-Lazerbeak (repurposed from Real Gear Booster X10)
-Skywarp
-Frenzy
-Starscream ***
-Ravage
-Rumble
-Thundercracker
-Buzzsaw (not in my collection, as far as I know no classics update)
* There is also, if it suits your tastes better, a second third party Reflector. There is, technically, an official one coming soon. But as a Targetmaster type figure with only a single robot mode (rather then splitting into three robots) it does not work as Reflector to me. I'll likely have it, as it comes with another figure I do want, but it will not be
my Reflector.
** Normally, I try to always go with first party figures when they are available, and there was an official, general retail Acid Storm with a green camo deco, but he seemed pointless to me without the other two. There were recently official Rainmakers made as an expensive convention exclusive, but I am unlikely to ever have those. I had these CHMS ones before the convention exclusive set was made, if the official versions had come first I would likely have just gone without. But already having these, I wasn't about to just throw them out.
*** Yeah, he's anachronistically sporting his coronation gear in robot mode... But what the heck? It looks cool.
There would be other characters who would technically be from Season One, such as Jetfire, or the Dinobots. But they were not Arc occupants (or other random generic Decepticon jets) and thus, in my collection, fall in with the "Other Pre-Movie Figures."
Autobots:

-Powerglide
-Jetfire
-Seaspray
-Inferno
-Silverbolt
-Warpath
-Tracks
-Red Alert
-Smokescreen
Also Pictured:
-Breacher (on Seaspray's back) - technically not a G1 character, but he works too well with this Seaspray toy to
not have with him.
-Drift (between Warpath and Tracks) - A G1 character, but not from the cartoon or the original toyline. Seemed to fit best (in my collection) with this group, so in he went.
-Hubcap (between Tracks and Red Alert) - not a G1 character, but too awesome not to have! (Reprolabels make him homage G2 Volt.)
In addition to the above, there are two minibots from the '85 toyline that I didn't include in the above photo. But they are included in this photo:

-Beachcomber (top row, far right)
-Cosmos (bottom row, far left) (Cosmos is getting another Classics style update soon.)
Pre-movie Autobots not in the above photos, but in the G1 toyline:
-Grapple (he does have a Classics toy, see Hauler above)
-Skids (getting a Classics style update very soon)
-Hoist (recently got a Classics style update, I acquired it after having taken the above photos.)
-Grimlock (does have a Classics figure, and I do own it, but I neglected to include it in my photos.)
-Sludge (no Classics update I am aware of)
-Swoop (no Classics update I am aware of)
-Slag (no Classics update I am aware of)
-Snarl (no Classics update I am aware of)
-Topspin (third party option available)
-Twin Twist (third party option available)
-Roadbuster (no Classics update I am aware of)
-Whirl (getting a Classics style update very soon)
-Blaster (see my next post)
-Perceptor (see my next post)
-Omega Supreme (some may use a repurposed "Year of the Snake" Omega Supreme, for others there is a third party option)
-Power Dashers (three figures, had no appearance in cartoon, no Classics update I am aware of)
-Omnibots (three figures, had no appearance in cartoon, no Classics update I am aware of)
-Air Raid (third party option available)
-Fireflight (third party option available)
-Skydive (third party option available)
-Slingshot (third party option available)
--The previous four, along with a third party Silverbolt, can form the gestalt Superion. (One can also repurpose a Revenge of the Fallen Superion if they don't wish to go third party.)
-Blades (no Classics update I am aware of)
-First Aid (no Classics update I am aware of)
-Groove (no Classics update I am aware of)
-Hot Spot (does have an official update, which I do not own, via a recolour of the Inferno mold)
-Streetwise
--The above five would theoretically form the gestalt, Defensor. The officially released Hot Spot mentioned is not designed to form part of a gestalt.
Decepticons:

-Blitzwing
-Thrust
-Ramjet
-Onslaught
-Octane*
-Astrotrain
-Durge
*Technically, Octane is a post-movie character, but I wanted to keep my Decepticon Triple-Changers together.
Also Pictured:
-G2 Megatron (between Astrotrain and Durge) - Why not?
-Lugnut (to the right of Durge) - Like Drift, a G1 character not from the original cartoon or toyline.
-Divebomb (to the right of Lugnut) - not a G1 character, but like Hubcap, too awesome not to have!
Pre-Movie Decepticon Gestalts:
(I am waiting on the Stunticons before taking a photo of these figures in the style of the other pictures I am presenting here, but here is a random photo of them, in gestalt mode only, that I do have.)

-Devastator (made from Bonecrusher, Hook, Long Haul, Mix Master, Scrapper, and Scavanger) (MakeToys)
-Bruticus (made from Brawl, Blast Off, Onsaught, Swindle, and Vortex) (as pictured, a mix of official Has/Tak and Fansproject. Technically possible to make a Bruticus using only Has/Tak.)
Pre-movie Decepticons not in the above photos, but in the G1 toyline:
-Bombshell (third party option available)
-Kickback (third party option available)
-Shrapnel (third party option available, getting a Classics style update very soon)
-Barrage (third party option available)
-Chop Shop (third party option available)
-Ransack (third party option available)
-Venom (no Classics update I am aware of)
-Shockwave (well, Devastator is pictured holding a third party Legends class offering. There are a few third party figures or popularly repurposed figures, but none yet that say "Classics Shockwave" to me, personally)
-Breakdown (third party option available)
-Dead End (third party option available)
-Drag Strip (third party option available)
-Motormaster (third party option coming soon)
-Wildrider (third party option available)
--The above five figures form the gestalt, Menasor.
Wow, this is getting long. Well, I think this should be a comprehensive list of what figures there are for characters from the first two seasons.
For any figures with the notation, "no Classics update I am aware of," if there is a third party option, or a popularly repurposed figure, I hope other people reading this feel free to point them out.
I shall break here, and be back hopefully tomorrow with figures from the movie and beyond. (This will include the above omitted Blaster and Perceptor, who were both in the show and the original toyline
before the movie, but which I felt looked better on my shelves paired with the movie/after movie figures.)
Note to other forum members: This was a
long post! If you wish to quote it in replies, please edit the quote to only include the relevant part you are responding to. Thank you!