I'm going to preface this with an admission that might 'lessen' my status as a Voyager fan in some people's eyes: compared to both DS9 and TNG, I've only ever seen the series 'in chunks'.
Having admitted that, my choice for my 'favorite Voyager episode of all time' goes to "Think Tank".
My favorite aspect of Think Tank is its storyline, which really gives Seven a chance to shine as a character outside of her role as a 'former Borg drone who still acts and thinks like a Borg' and also really hammers home the depth of connection that exists between her and Janeway.
I also really like Jason Alexander's role in the episode; I became a fan of his due to the voice work he did in Aladdin: The Return of Jafar
and Aladdin: The Series
and his role in Disney's live-action production of Rodgers and Hammerstein's Cindrella
, so it was great to see him show up on Voyager. Plus, his character really reminds me in many ways of John Delancie's Q.
Note: I haven't seen either of Delancie's two appearances on Voyager, so the above comparison is being made based solely on his multiple appearances on TNG and his lone appearance on DS9.