Coffee Cups: 2

Wondering where all that coffee actually goes to? Chakotay gives a medical demonstration. Don't try this at home, folks. It's a trick which should only be performed by trained professionals. Shortly after drinking this cup of black coffee all his hair fell out.
Scientific Method

Tom and B'Elanna hit the coffee after sitting through a couple of hours of the Doctor's photographic slideshow. Whether it's an essential wake up call or just because the craving gets too much after a couple of coffeeless hours I don't know, but judging by the cups Neelix has lined up he clearly expects considerably more customers to follow.
Nothing Human

Hitting the coffee for its rejuvenating properties after a rough night, Tom looks as if his nightmares are continuing even while he's awake. In fact, this cup is labouring under a false identity: Neelix has accidentally poured him a steaming cup of cooking oil.
Waking Moments

While researching her ancestor Shannon O'Donnell, Janeway learns some shocking facts. We learn more. O'Donnell, who has the coffee fixation enough to drink the stuff while driving along in her car, married Henry Janeway despite the fact that the only coffee he offered her was decaf. Clearly his was the recessive coffee gene in the family...
11:59

You'd think that the caffeine alone would be enough to keep someone awake through the dead of night, while they work on that tedious report that they've put off until the last minute. But Neelix brings out his special fire nut blend of coffee for Harry, promising that it'll keep his eyes open. Now if it would only do his homework as well...
Mortal Coil

Paris, Torres and Neelix discuss insurrection strategies over a cup of coffee, trying to come up with the most effective way of joining holoChakotay's unhappy little band without getting themselves toasted. Hopefully some of those ideas come in handy later, when Paris and Tuvok are trying to keep out of holoSeska's way long enough for the coffee-fuelled brain of their captain to rewrite the plot along lines with a lower body count.
Worst Case Scenario

It may still be a Starfleet ship, but rules and regulations have relaxed enough on Voyager nowadays that people have occasionally been seen at their posts in civilian clothing, or even bringing drinks to their posts to sip while they work. Of course, it might help Paris's case, when marching boldly in with coffee mug in hand, that the Captain's a big fan of the beverage in question. I just hope he doesn't spill it into any of those sensitive panels if the inertial dampers should accidentally go offline in the course of his duty shift...
Waking Moments

Kathryn Janeway makes good use of her normal source of inspiration as she ponders a plan for rescueing Seven of Nine from the Borg Queen.
Dark Frontier

Kathryn Janeway pauses during her first ever tour of Voyager to test drive the replicator in her Ready Room. Her order? Coffee of course. And they're not even out of dry dock yet.
Relativity

Chakotay and Kim talk engineering matters with the Equinox's Ensign Gilmore. Is she using the coffee they're drinking as creative inspiration for ways not to tell them what naughty things her crew have been up to with their warp core?
Equinox: 1

Max Burke feels the call of Voyager's mess hall. I guess after five years on replicator rations, it's not surprising. And yes, there's definitely a coffee cup to hand. Maybe they should have tried that in Equinox's warp core instead of the Ankari sky spirits.
Equinox: 1

Janeway debates the science and tradition of various cultures' religions and spirit quests with Chakotay. Is it just coincidence that she happens to have a cup of the stuff that she herself worships in hand while she does it?
Sacred Ground

B'Elanna Torres sips coffee while she debates life, death, and mysterious Klingon artifacts that appear in the Delta Quadrant and damage shuttlecraft with Chakotay. Better keep an eye on those artifacts though. If you turn your back on them to refill your coffee cup, they're likely to bleed all over your coffee table.
Barge Of The Dead

Serving coffee at meetings is more than just good hospitality. It's also a handy demonstration tool. Tash shows Janeway and the crew how he hopes his space catapult will get his ship (and theirs) a little closer to home in next to no time, in a way that the captain is guaranteed to pay attention to.
The Voyager Conspiracy

A little down time, cuddled up with a drink and a Klingon romance novel. But is the approaching Tom Paris after the coffee, or the chance to sneak a read of Woman Warriors at the River of Blood? Probably the former. After all, B'Elanna assures us that her book isn't a technical manual...
Real Life

Janeway uses epicurean diplomacy on the crew's pleasure-seeking host. She's hoping that her marvellous pecan pie recipe can be exchanged for a 40,000 light year boost closer to home. Sadly, not even the accompanying coffee is able to achieve that.
Prime Factors

Astronaut Gotana Retz comes from a planet that exists in a different timeframe. As a result, he sees Voyager in slow motion. But Neelix pouring Janeway a cup of coffee is the kind of timeless moment you don't really need freezeframe to see in just about every episode.
Blink Of An Eye

Commander Chakotay indulges himself in a cup of the usual while his fellow senior officers debate the chances of the competitors in the Tsunkatse tournaments. Perhaps he's also pondering upon the best time to tell B'Elanna that he's taken her suggestion about delegation to heart, and that the new roster has her on bridge duty while he attends the match.
Tsunkatse