In one JLA story (JLA #61), Batman gives the Flash what is supposed to be a reassuring hand on the shoulder prior to briefing Flash on his role in the plan. Flash's response: "You're touching me. Batman is touching me. I'm going to die, aren't I?"
"Not if you pay close attention."
As I recall, the plan involved Flash riding one of Batman's missiles into an enemy target. The look on his face was priceless.
Also from that issue, a great one-liner upon discovering a familiar villain in the midst of his villainy:
Wonder Woman: Abra Kadabra!
Green Lantern (singing): Gonna reach out and grab ya...
In JLA: Year One, J'onn transforms into Superman without anybody noticing and appears sitting at their conference table after the other members had been talking about asking Supes to join. After they stare at him in shock he then turns into ELMER FUDD. Especially funny because he has been quiet and relatively humorless up until that point.
J'onn J'onzz: You're vewwy vewwy qwiet. "Yoda! Do Yoda!"
Gail Simone's JLA comic The Hypothetical Woman has a scene where the League is planning their next move aboard the Watchtower...and while they're doing that, Wonder Woman surprises everyone with pomegranate cookies that she baked herself.
GL/Flash: Wonder Woman BAKED?!
And at the end of the scene:
Batman: Diana, Alfred will need that recipe.
Post-Flashpoint Justice League has the first meeting between Green Lantern and the Batman, having Hal ask what Batman's powers are before saying, "What, you're not just a guy in a costume, are you?" Batman responds by taking off Hal's ring.
And later, the Flash: "Batman doesn't have any powers? I thought you were a vampire or something."
This exchange in Justice League #4:
Wonder Woman: We need to get those men out of the helicopters and somewhere safe.
Green Lantern: I'll get them out of the choppers and to safety. Not to be a good guy like the Flash, but because I want to impress you. Most of what I do is about impressing people.
GL: No, I... what'd I just...?
WW: You were touching my lasso.
GL: So what?
WW: It makes you tell the truth.
GL:[looking off-panel] Are you laughing, Batman? At a time like this?
The cover of the in-universe book "Justice League: Gods Among Men" by the fictional David Graves. It features the Justice League fighting Starro (as a Shout-Out to the League's original comics appearance)... except for Flash, who's incapacitated in the monster with a starrosite on his face, while everyone else poses like badasses. It's almost as if whoever illustrated the cover forgot the Flash was a member of the League until halfway through drawing the layout, at which point he just squeezed him into the picture's remaining space.
Pretty much any of Green Arrow's attempts to join the League in issue #8.
In (Grant Morrison's) JLA #9, Green Arrow (Connor Hawke) stumbles upon everyone in The Key's Lotus-Eater Machine. The Key destroys GA's equipment, forcing him to use his father's old stuff.
The same issue marks the first time Batman in Morrison's tenure that Batman directly addresses rookie Green Lantern Kyle Rayner:
"Nintendo has a lot to answer for."
In the "Rock of Ages" storyline, Flash, Aquaman, and Green Lantern are hurled into the future and they come up with a plan to use Flash's speed and a device they find to get back.
Aquaman: What's likely to happen here, Flash? We seem to be moving very fast, very quickly... Can we take this kind of acceleration?
Flash: This is jogging. But when I hit top speed, then the treadmill takes over, amplifies my velocity and we hit... I don't know... faster than light squared... We're accelerating to speeds where our entire physical structures will be converted to hyperlight information!
In JLA: Primeval, the team gets hits with rays that devolve them. Wonder Woman's clay body falls apart, leaving her as a disembodied spirit. But at least she still has her mental faculties, so she tries to gather the others, including big, scary versions of Aquaman and Superman, an amorphous blob (Martian Manhunter), and several cavemen. Then they get to Zauriel, who has turned into a mischievous, blonde-haired cherub who giggles and throws apples at people. The cavemen laugh, and even Wonder Woman is forced to admit that it's pretty funny.
In JLA/The Titans, a number of heroes are flying up to a huge orbiting station constructed by Cyborg that is causing global disasters. Martian Manhunter is in telepathic contact with Oracle.
Oracle:(telepathically) How are the additions to the JLA cavalry working out? Is Gardner making an ass of himself yet?
Martian Manhunter:(telepathically) All assistance is appreciated. Just make sure everyone is in place, Barbara.
Guy Gardner:(aloud) Damn. Nasty here is big. Good thing you brought me along.
One storyline begins with Green Lantern and the Flash calling the rest of the League. They report that seven supervillains are attacking the White House! The rest of the League rushes there, expecting a massive Villain Team-Up and find... all the supervillains beating each other up. Turns out all the villains hit upon the same scheme of attacking the White House, all showed up at the same time by sheer chance, and than got into a brawl with one another for "stealing my idea!". Lantern and Flash just needed help getting civilians out of the way.
JLA #27: Bruce Wayne is meeting Clark Kent in Tokyo. Clark is with another woman who is introduced as Hino Rei. Bruce immediately recognizes that she's really J'onn, because the name gave it away.