Re: If you had to pick your two favorite Voyager Episodes...
Picking only 2 is difficult, but-
Distant Origin Season 3
An alien paleontologist discovers a common ancestral link between his people and humans. He believes that this proves that his people (the Voth) evolved on Earth and migrated to the Delta Quadrant millions of years ago, but his government is not as willing to believe his interpretation of the evidence.
Living Witness Season 4
700 years into the future the Doctor must defend the crew of Voyager and set history straight when an alien race claims that the Warship Voyager was responsible for war crimes commited against their race.
And I'll cheap by offering 2 runners up-
'Hope And Fear" season 4
An alien translator by the name of Arturis is able to finally decode the Starfleet message received by Voyager five months ago. It tells them to go to a new type of ship waiting for them with an engine system faster than warp drive, which is capable of bringing them home within three months.
"Memorial" season 6
The crew of Voyager experience vivid memories and dreams of a battle they don't remember having, with an enemy they have never encountered.
I would've picked Caretaker, as it still ranks for me as the best of the Trek pilots, but you might have counted that as 2 eps instead of one.