Coffee Cups: 1

The cup of coffee that killed Tom Paris. Of course, it turned out that he was actually allergic to the water in the coffee, rather than Neelix's latest fiendish blend itself, but that doesn't make nearly so good a story.
Threshold

What is that crawling out of Neelix's coffee pot and into Kathryn Janeway's cup? Neelix's "better than coffee" coffee substitute of course. No wonder Janeway finds a hasty excuse to be somewhere else...
The Cloud

It would appear that Neelix's culinary urges extend even to a bit of in-shuttle catering when he's on away missions... particularly when he's sharing the shuttle in question with coffee's greatest fan, the captain. I just hope that all those consoles are protected against accidental coffee spillage, or there'll be another damaged shuttlecraft for B'Elanna to repair.
Macrocosm

Chakotay has many fiendishly clever tricks to call upon in order to keep his captain happy. He knows how to build bathtubs, and headboards. And he also knows the wisdom of bringing a coffee supply along (or at least a fully charged replicator) when you think you're going to be stranded alone with her on an isolated planet in the Delta Quadrant for life.
Resolutions

No one in their right minds would go to Planet Hell if they could drink coffee instead. So Janeway, the ultimate control freak, chooses to delegate and send Paris and Neelix instead. Meanwhile, all of their replicator rations will be going on getting that hair pasta removed from their clothes.
Parturition

A busy day in Sickbay. Nothing to do except fix Seven's lacerated hand and nurse Harry Kim through a bad case of puppy love. So Tom Paris, newly reappointed nurse, kicks back and puts his feet up with a nice jug of coffee.
Revulsion

When you're cruising at high warp through a two year stretch with no view and no aliens snapping at your tail, you have to create your own amusement. So Tom and B'Elanna play Derata and snap at each other in the middle of the night. Is it the boredom, or is Tom just following his Captain's example and overdosing on caffeine?
Night

Cosimo introduces Harry Kim to the pleasures of Vulcan Mocha, extra sweet. But, perhaps Harry doesn't have an excessively sweet tooth? He certainly seems to be able to talk himself into heading back to the Delta Quadrant and the kind of coffee that only Neelix could make...
Non Sequitur

B'Elanna ponders creative engineering solutions to the problem of the warp nacelles falling off a shuttlecraft when it hits warp ten. Whether the coffee's responsible for the eventual solution, or just for her, Tom and Harry trying to hit warp ten in the first place is anyone's guess.
Threshold

Janeway may love her coffee, but her expression here clearly says that she doesn't like other people taking liberties with her ship, her ready room, or her coffee supply. Kashyk is probably right that the way to Kathryn Janeway's heart is through her coffee, but he shouldn't really be helping himself to it via her replicator (and presumably her replicator credits).
Counterpoint

For those who've always wondered what use Janeway, the galaxy's most enthusiastic coffee drinker, has for a silver tea service in her Ready Room, the answer's simple. She drinks coffee out of it. Here she is, caught in the act, inviting Chakotay for coffee and boasting about its Borg beating properties.
Hunters

It probably comes as something of a shock to realise it... but Kathryn Janeway wasn't the first person in the series to be seen wielding a coffee cup. Tom Paris managed to steal a march on her, by swigging raktajino in Quark's bar prior to rescuing Harry from Quark's clutches. Janeway's first coffee cup shows up slightly over a minute later.
Caretaker

What do you do when your ship is stuck on a subspace sandbar, your holodeck is being invaded by creatures from another dimension who think that the program's arch-villain is real and you're not, most of the replicators are down, and the sonic showers and toilets are rapidly following them? And you have Bolians aboard? You hit the coffee. And you refuse to let anything or anybody get in your way before you've had that first sip.
Bride Of Chaotica!

On the Doctor's orders, Seven investigates as aliens only she can see experiment on her fellow crewmembers. She could take a few lessons in acting naturally though. Since she only started taking real food and drink in the previous episode, and didn't react well to it, some might find it suspicious that she's picked up the coffee habit so very quickly...
Scientific Method

Ensign Samantha Wildman partakes of Neelix's brew. Is it only coincidence that several minutes later she starts giving birth to the first child aboard Voyager, or something entirely more sinister in the coffee that helps Naomi on her way?
Deadlock

Strange though it may seem, there are occasions when even Kathryn Janeway has been known to turn coffee down. During the search for the missing Delta Flyer she declined Neelix's in-Bridge catering with the comment that one more cup and she'd go to warp.
Once Upon A Time

B'Elanna's creative fuel, particularly on sleepless nights when she has androids to revive, is coffee. Neelix stops her after two pots. Probably just as well, since she admits to having found his Landros blend "almost palatable".
Prototype

Janeway's first sighting with coffee cup in hand, going over system status reports as Voyager prepares to leave DS9 for that fateful mission to the Badlands. If she'd known what was in store for her, she'd probably have been drinking it by the jug instead of the cup, overdosing on the stuff while she still had the chance!
Caretaker

Even holographic Doctors can catch the coffee bug. The Doctor creates himself a holographic family, as part of his quest to educate himself about humanity and relationships, and the holographic wife he gives himself replicates him exotic new blends of coffee from Paxor 3. He says that it's quite good, but then again we don't know if he's programmed himself any taste buds yet.
Real Life

When you need to outthink a think tank, you can do a lot worse than lock your entire senior staff in the mess hall with an endless supply of coffee and keep feeding them caffeine until they come up with the necessary inspiration.
Think Tank