Best Non-AO3

At Any Cost by quantumsilver - cw: torture, angst, lots of hurt/ some comfort, Tom & Janeway POV very psychological thriller vibes

Bend it by Carkins Bug - Rated M. Time travel hijinks with Chakotay narrating makes for an uproariously fun read.

Confessions by Nynaeve506 - oneshot: delightfully drunken Janeway with only Tom Paris to deal with her and her drunken truth-telling

Contrition by Michele Masterson - MCD, Angst w/Happy ending, B'Elanna POV

Equinox At the Gate of Daybreak by ForceForGood - part of a series, but very readable as a standalone

Finding Peace by Monkee - AU Voyager return, angst and romance, Chakotay centric

Holodeck Safety Protocols by Jemima - Romance, holographic misunderstandings, and an EMH who really should leave the Sex therapy prescriptions to someone else. Dub-con only if you squint.

The Cardassian Mask by LR Bowen - Set end of season one, through season 2. novel length adventure / romance

The Dance by Jemima - romantic and fun throughout. Tom POV and his humor is sprinkled through

The Only Constant by MissyHissy - Novels Fic! set after Pocket Full of Lies. Angsty Romantic JC!

The Subtle Art of Timing by Megara79 - Rated M sexy smutty x-mas story

The Water is Wide by Isle of Avalon - a beautiful angsty romance set mid-series, about a JC who need to lose each other to find their way back together.

Winter's Child by J. Elisabeth - AU result of Timeless - if there had been survivors of Voyager's crash in the unaltered timeline. Angsty hurt/comfort and a dash of romance sprinkled on there.