Pinky, Elmyra, and The Brain contains examples of the following tropes:
All Love Is Unrequited: Elmyra has a crush on a slob named Rudy Mookich (apparently forgetting about Montana Max), but Rudy has the hots for her cousin Patty Ann — who is really just Brain in his mechanical suit. Brain, needless to say, does not return Rudy's affections, but Elmyra seems to think "she" does.
Brain: Any questions? Pinky: Just one. If Fred Flintstone knew the giant order of ribs was going to tip over his car, why did he order them every week? (later) Brain: It was an end title. Pinky: What? Brain: Fred Flintstone doesn't order ribs every week. That was only animated once, then music and voice tracks were added. The footage is run at the end of the show in the same spot every time. It's called an end title.
Artistic License - Economics: One of Brain's schemes to take over the world involved getting all of the money in the world for himself. However, if one person had all the money in the entire world, cash would become useless, and people would naturally resort to other forms of currency for exchanges.
Berserk Button: Don't get caught cheating in front of Baloney. Don't let his ability to tolerate anvils fool you, you will not like the result.
Biting-the-Hand Humor: The opening song features the line "It's what the network wants, why bother to complain?" At the end of the song, Brain says "I deeply resent this."
Calling Me a Logarithm: Elmyra has a tendency to mistake Brain's technical jargon for "naughty-waughty potty talk".
Chuck Norris: Elmyra goes to Chuck Norris Grammar School (instead of Acme Looniversity).
Credits Gag: Similar to the Credits Gag of the original series, the credits here have Elmyra attempting to define the words instead, and we end up with things like the word "onomatopoeia" being defined as, "Naughty potty word!"
Express Lane Limit: In one episode, Brain tried to become a masked hero to get people to respect him. One of his attempted good deeds was preventing a man from using the express lane with one item above the limit. Nobody cared.
Rudy Mookich is pretty much Nelson Muntz without the "Haw-haw!" In fact, acording to the author of the most extensive article on this series over at platypuscomix, they even share the same voice actor.
Retcon: As if it wasn't enough that this series was basically an unneeded Re Tool to a show that was doing fine the way it was, practically everything else about Tiny Toon Adventures is never mentioned. The show's setting was Pinky and the Brain mixed with that of a scrapped Elmyra-based Tiny Toon AdventuresSpin-Off.
Self-Parody: The writers even take shots at the new direction in the theme song.
One episode opens with Mr. Pussy-Wussy chasing Pinky and Brain, who are shown respectively wearing a vest and a bow-tie, ŕ la Pixie and Dixie from The Huckleberry Hound Show.
Pinky: Egad! That cat hates us meeces to pieces! Doesn't he, Mr. Pixie? Brain:Stop calling me Mr. Pixie! This isn't funny, it's sick!
In one episode, Elmyra talks about spelling something with "lots of Qs". It's a reference to a mid-1990s Flame War on alt.tv.animaniacs (and particularly, its associated IRC channels) over a Verbal Tic that got out of hand.
Stupid Question Bait: This happens Once an Episode. The Brain explains the plan of the episode, then asks, "Any questions?" This prompts Pinky to ask a completely irrelevant question. It isn't until the end of the episode when the Brain answers the question. For example, when Pinky asked why Fred Flintstone keeps ordering giant ribs every week, the Brain explains the concept of end titles at the end of the episode.
Stylistic Suck: "How I Spent My Weekend" is drawn and narrated by Elmyra.
Tastes Like Diabetes: invoked (In-show) Brain complains about Elmyra's selection of albums, which contain such titles as "It's a Sugary-Wugary Day" by Laffi and "Life's a Rosy-Posy Bed of Honey" by Mary Flewis and Porkchop.
Brain: Let's see... Where to begin... Ah, yes, Uranus is gaseous. Elmyra: *Gasp* Naughty mousey big head, musn't use naughty potty dirty words! (washes Brain's mouth with a bar of soap)
Vandalism Backfire: Elmyra once stepped on Rudy's snake to force it to spit Pinky and the Brain out. Rudy tried to retaliate by stomping on something of hers but stomped on Brain's device of the week. After she told him it wasn't hers, Rudy simply gave up and left.