Name That Episode, VOYAGER Edition...

[Brennyren]

Your neurogenic interface is trying to kill you.

Clue 1. It all started where it always does.
Clue 2. An unusual choice of name.
Clue 3. Practice does not always make perfect.
Clue 4. Paris, you look different.
Clue 5. That doesn’t look like work. (But it is.)
Clue 6. Sometimes an engineer needs to narrow things down.

Clue 7. Tries to replace an old family with a new one. Eventually succeeds, kinda.

 

[Brennyren]

Clue 8. Haven't seen those outfits in a while.

 

[Farscape One]

"PATHFINDER"?

Barclay names his cat Neelix, which Troi says is odd. We see Chakotay and Torres in their Maquis outfits.

 

[Brennyren]

"PATHFINDER"?

We have a winner!!!

Clue 1. It all started where it always does. Since the episode focuses on Barclay, that means the holodeck. He even says so, and in more-or-less those words.
Clue 2. An unusual choice of name. As you said, @Farscape One, the cat named Neelix.
Clue 3. Practice does not always make perfect. Seven refuses to give Neelix (the Talaxian, not the cat) any more singing lessons. He protests that he's been practicing. She says it will not help.
Clue 4. Paris, you look different. Admiral Paris, previously played by Warren Munson, is now played by Richard Herd.
Clue 5. That doesn’t look like work. (But it is.) Suspicious as it looks, Barclay really does use his holographic simulation to refine his ideas.
Clue 6. Sometimes an engineer needs to narrow things down. To make his plan work, Barclay applies a narrowband filter to the signal.
Clue 7. Tries to replace an old family with a new one. Eventually succeeds, kinda. Missing his Enterprise family, Barclay finds solace in the holographic Voyager crew. When he succeeds in communicating with the ship, the real crew make him an honorary crewmember.
Clue 8. Haven't seen those outfits in a while. In Barclay's program, Chakotay and Torres are in their Maquis leathers.

Congrats, @Farscape One! You win the privilege of being the next clue-giver!

 

[Farscape One]

Thanks.

Here we go...

1. Seven did not find the answer.

 

[Brennyren]

"Body and Soul"?

 

[Farscape One]

Your program has been obliterated.

 

[Brennyren]

....but I'm too young to decompile!

 

[JirinPanthosa]

Omega Directive

Knowing Farscape he might be being tricky and referring to seven different people who did not find an answer.

 

[Farscape One]

Your warp drive is permanently gone due to Omega's destruction.

(Am I really that tricky? )

 

[JirinPanthosa]

I have to try it.

Think Tank. Seven crew members could not figure out the puzzle. Only Seven could!

 

[Farscape One]

You are lost in thought.

Next clue...

2. Shouldn't have been on this shuttle.

 

[Brennyren]

"One Small Step." Seven did not want to make the trip, she was ordered to.

 

[Farscape One]

One large step into wrong.

 

[Farscape One]

Next clue...

3. Time is an enemy and a friend.

 

[JirinPanthosa]

Timeless

 

[Farscape One]

You crashed to an icy death.

 

[Brennyren]

"Relativity." Braxton keeps using time-travel to escape, while Seven and the others use it to head him off.

 

[Farscape One]

The Kazon destroyed you.

Next clue...

4. The only time he wears it.

 

[JirinPanthosa]

Once Upon A Time