I think Voyager's look should have varied over the years.
At first (on the advise of Starfleet counselors at the Utopia Planitia) Voyager is painted a nice friendly pink to encourage non-hostile reactions. However this is increasingly obscured by black scorch marks from high-velocity weapons-grade particle impacts and tractor beam deformation. By the end of Voyager's first season the hull looks like Galactica's in BSG's Season 3. Minus the gun turrets and nuclear missile launchers. Which are shown under construction.
Phage through to Deadlock: Voyager is covered in yellow and black warning stripes, plus signs in Vidiian saying: QUARENTINED DUE TO HIGHLY CONTAGIOUS FLESH-EATING ORGAN-DISSOLVING VIRUS.
Tattoo: Before Voyager descends into the atmosphere, the crew paint a large tattoo on the front to show their good intentions.
Resolutions: To commemorate their new captain the crew give Voyager a pair of enormous latex 'Spock' ears, plus something long and black slung underneath (a phase cannon of course! Tuvok's into security you know...what did you think I meant?)
Basics: Kazon colours, which have to get repainted every day as the sects change.
Macrocosm: I don't know about the outside, but the interior should be done up like the Nostromo with grimy bulkheads, condensation and clanking chains. And a cat.
Before and After: Voyager's undersection gets infected by a space moss with long hair-like tendrils. When Kes is older, so the 'beard' is longer and greyer. As she goes back in time it reverts to a younger 'peachfuzz'.
Worst Case Scenario: In the Maquis mutiny scenario the words "F**k the Ocampa! I Want To Go Home!" are spraypainted across the bulkheads. When Seska takes over the graffiti reads "Bajor Is Cardassia's Bitch."
Scorpion: The Kazon colours reappear, in the hope that Voyager will appear unworthy of assimilation.
The Gift: For fraks sake, leave the Borg armour on!
Year of Hell: Disruptive pattern camouflage.
The Killing Game: Swastikas on the nacelles.
Living Witness: Evil Voyager is jet black and silver. The deflector dish bears a suspicious resemblance to a certain depression in the surface of the Death Star.
One: Voyager's hull is slowly scorched as it passes through the radioactive nebula. In the last act we see a closeup of the name and registration number being burnt away.
Hope and Fear: Panels rip off and tumble into the slipstream as Voyager tear-asses after the alien who kidnapped Seven and Janeway.
Night: The ship is dirty reflecting the captain's increasing apathy. When Janeway starts to kick ass again, the hull suddenly turns a blinding white and the warp engines rev in approval.
Extreme Risk: Tom's beloved dynametric tail fins appear, until Tuvok curtly insists on their removal.
Timeless: For the quantum slipstream test Voyager is painted red. As in 'redshirt'.
Counterpoint: Imperium inspection stamps mark the hull. Plus graffiti by xenophonic Devore soldiers – an arrow pointing to Voyager's plasma intake and the words "Gaharay vessel – Insert d**k here."
Bride of Chaotica: A B&W Voyager wobbles along on wires while sparks flare from its engines. In another homage to Flash Gordon, the ship emits a constant farting sound.
Bliss: The deflector dish curls up in a huge beautific smile.
The Disease: Voyager is covered by a giant condom, like Leslie Nielsen in Naked Gun.
Course: Oblivion: Voyager's colors run in the opening credits (foreshadowing).
Barge of the Dead: Klingon symbols, which disappear after B'Elanna blinks hard and rubs her eyes.
Pathfinder: We see Voyager as envisioned by Reg Barclay. A kind of Pimp Your Ride version.
Fair Haven & Spirit Folk: Voyager is painted green for St Patrick's Day.
Blink of An Eye: More graffiti by alien astronauts: "Boldly Going Nowhere Fast".
Virtuoso: The crew erect a gleaming white opera dome on top of Voyager, which unfortunately bears an uncanny resemblance to a certain Doctor's head.
Collective: After this episode Voyager's hull has chocolate fingerprints all over it, and toys keep getting left in the airlocks.
Live Fast and Prosper: Large sign saying "Accept No Substitutes."
Fury: Voyager gets flown apart, so no changes are necessary.
Drive: Racing stripes. And sponsor decals.
Flesh and Blood: The rest of the season begins with the Doctor scrubbing the hull clean with a very small toothbrush. Comedy episodes have a Jay Chattaway cover of the Red Dwarf theme, and the Doctor hanging on with a terrified expression whenever Voyager jumps to warp after the opening credits.
Shattered: All of the above. And everything to follow. At the same time.
Prophesy: Klingon graffiti, eg. "Kohlar's mother was a notch on Kirk's bedpost!" "The father of the kuvah'magh is a Federation pansy!" "Ch'Regha does it with Talaxian bar rodents." "I'm going to make that human captain my targ. She'll worship the length of my bat'leth! - T'Greth" "The only thing that redheaded bitch worships is coffee! – B'Elanna."
Q2: As a prank Q's son vanishes the nacelles and uses Voyager to stir a giant cup of coffee. Black, of course.
Author Author: In order to differentiate it from Voyager, the Doctor gives the starship Vortex a fake moustache.
Friendship One: It's finally revealed who's been outside all this time doing external hull changes. Lieutenant Joe Carey. However Janeway finally decides to let him go down to the surface to stretch his legs. What could possibly go wrong?
Endgame: Voyager's hull armor comes with 'bat' fins. In the homecoming celebrations scene, party lights and streamers cover the ship as it swoops over San Francisco.
