The Warden and Jared thwarting a large scale prison break in "Uh-Oh, It's Magic" with nothing but awesome magic tricks.
Combaticus is a walking example of this, EASILY ripping apart hordes of violent inmates without effort in his episode.
Pretty much any brawl sequence in Superjail, where the bodies pile up by the dozens.
Any episode in which either the inmates unite with each other or the administrators is guaranteed to be awesome, by virtue of the tag-team action and the probability that they're doing so to beat back a far more deadly foe.
In "Planet Radio" the final battle is against rats, so the Doctor turns Alice and several inmates into the characters from Cats, and they kick ass with ballet.
The final battle in "The Trouble with Triples" is one big shout-out to classic video games in general, with the inmates and staff fighting off alien creatures (which they believe are game bosses) with different techniques and power-ups.
The climax to "Oedipus Mess" has Jailbot traveling out to the outside world once more, to capture Jacknife. The only difference? There are at least 10,000 Jacknife clones loose note minus the two the Twins took off to another dimension. Jailbot proceeds to activate "Nano mode" and divide himself up into miniature copies so he can capture every Jacknife. One long bloody capture sequence follows, with all the Jacknife clones apprehended and torn apart from Jailbot's handiwork.
Jared and the Doctor fighting and rounding up the Doctor's escaped mutants in "Superfail", while attempting to rescue the Warden from the sewer facility (and a three-headed mutant dog that's taken an interest in him).
The Doctor breaking the Warden and Jared free in "Vacation", and the three proceeding to launch a rescue attempt on the inmates. Although they wind up captured by the Zamzazons, they still put up quite a fight with machine guns against the winged snake creatures.
"Sticky Discharge" has Paul decide that he doesn't want to return to the real world, and fight his way back into the jail by punching out Jailbot, and evading several deathtraps all so he can reunite with Jean.