I’ve probably been watching too much TV lately…
Point singularity bullet - Andromeda
Nova bombs - Andromeda
Sentry guns - Aliens (deleted scenes)
Ion cannon - Stargate: SG-1
Species 8472 roundup (ships merge energy to blow up planets) - Star Trek: Voyager
I don’t know the name of it but the new weapon added to the Enterprise in the final episode of the Star Trek: TNG(All Good Things) when they show the E in an alternative future. It has a new weapon that was able to take out a Klingon ship in just a few seconds. Cool.
Whoa, how can you forget the Death Star? Now that was groovy. Too bad they left the window open.
I always liked the hand-held weapons from Space:1999. They just had a cool look to them.
I’m also partial to light-sabers. “An elegant weapon from a more civilized time,” I think was the catchphrase. Cut a man in half while you look into his eyes, just the way it ought to be.
Star Trek weapons are generally pretty lame, but the phasers used in “The Wrath of Khan” and “Search for Spock” disintegrated people in a most spectacular and cool manner.
I thought the shadow planet-killer from Babylon 5 was really cool. For those who don’t know, it was a big black cloud that fired thousands of missiles at a planet, which would burrow to the core and explode, causing the planet to rip itself apart. Also it could suck all the energy out of any ship caught inside of it.
Unicron.
(From Transformers: The Movie)
Hey, I’ll take a stunner with a broad beam option and pretty good range any day.
Shoot first, ask questions later.
Mass Driver
(Moon is A Harsh Mistress)
There’s nothing like a rock. Hit something hard enough to generate alpha rays. Coool.
Let’s see.
Monowhip.
(Johnny Memnomic)
Okay, so, it just sort of slices between atoms. Can not be bad.
Sun Eater
(Legion of Super Heroes)
A giant nebula-like creature that eats suns. Again, simple, effective
Green Lantern Ring
(Green Lantern)
C’mon, what can I say?
Main Gun, SDF-1.
(Macross/Robotech)
There’s something about the first time you see a quadrant of space go foomp.
(Mildly entertaining space opera that looks more like a porno with the sex removed, but it’s a cool weapon/ship/organism)
Personally I like the mind control thing that “made” Kirk kiss beautiful women.
Jeez, can you imagine going back to your SO and saying, “Honest honey, I didn’t want to kiss those fantastic looking women. These guys in togas made me.”
Iain Banks has some pretty cool weaponry in his Culture stories.
Wynonna(John’s Gun): Farscape
I don’t know. Just gotta love a gun named Wynonna.
IIRC, that was a phaser cannon.
I liked the flechette rifles used in the Hyperion/Endymion saga.
James Woods automatic pistol in Videodrome isn’t very SF until he pulls it out of his stomach and it grows into his hand 
Star Trek’s weapons are pretty wimpy until it comes to the Genesis Device (ST Wrath of Khan). Not only does it completely wipe clean your enemies planet, it leaves it smelling lemon fresh and ready for recolonisation.
Or the illegal weapon held by Kivas Fajo in TNG. A disintergrator that works from the inside out. Cool.
The Reavers in Starcraft. Big insect like tanks that produce drones that fly out and whup the ass off anything in its way.
Talking of insects, the big bugs that shoot plasma out their ass at passing space craft in Starship Troopers One hellava party trick!
For massive massive weapons read Ian Banks Culture novels. Especially the destruction of the orbital in Consider Phelbas. (Haven’t read it in ages, its late, excuse any possible errors in spelling)
Monofilament weapons, ala Johnny Mnemonic.
Mass drivers, like the Centauri used to devastate the Narn homeworld in Babylon 5. Nothing like dropping a five mile rock on a guy to let him know who’s in charge.
Star Destroyers: Okay, the Death Star was big and all, but these suckers just rocked. The deadliest looking spaceship ever.
The Carrier, from the comic The Authority. A giant, inter-dimensional alien space-ship. At one point, they kill a supervillain by crashing the ship into the city he rules. Ship: 1 Skyscraper of Evil: 0
The battlesuits from Starship Troopers, which turn every soldier into a one-man tank. (I’m talking about the book here, obviously)
Major Motoko, from Ghost in the Shell. Grrrr.
Most of the Klingon bladed weapons…man, they just have style.
Han’s blaster pistol. Lightsabers are cool, but ancient weapons and hokey religions are no match for a good blaster in your hand, kid.
X-Wing fighters.
And of course, the most subtle Sci-Fi weapon, a slightly off-kilter HAL 9000 unit.
Larry Niven came up with some really good ones:
The Tasp --(in ** Ringworld**, among others)-- control your enemies by overwhelming them with pleasure.
The Variable Sword – the closest thing in literary sf to Star Wars’ Light Sabers. It conssed of a wire encased in a stasis field. As the name implied, it could be made any length, and was virtually indestructible.
The Sinclair Molecule Chain. Niven was writing about monofilament line weapons back in the '60s, well before Johnny Mnemonic. The SMC wasn’t used as weapon in the earliest stories, but it showed up as one in Ringworld
In The World of Ptaavs they had a device hat excavated by “suppressing” the charge on an electron, making the positively-charged nuclei fly apart. It made a nifty weapon, too.
My favorite weapon goes to the PPG on Bablyon 5. I love the sound the gun (any of them will do, the bigger the better) when they power up
For a close second I’ll have to give it to The Lawgiver(spelling? name?) from Judge Dredd the movie. Lots of cool option and the…
…
DOUBLE WHAMMY
Personaly, i just want one weapon… a Bolo Mk XXXIII