I only have a bit of proof (when compared to other sites XD). If you would like, you can send me some. I'll credit you.

.OFFICE.
Wally was originally going to escape without the girls, but he changed his mind when he found out Kuki was there.

When Wally is left on the rocket ship, Kuki calls out his name.

.GROW-UP.
In the credits, Wally was handing Kuki a popsicle.

Also in the credits, Wally and Kuki were leaning against each other as they looked at the stars.

.CATS.
When Wally is being pulled in by the cats, with what could be his last words, he says, "Tell Numbuh Three I'm sorry!"

Even after saying Wally deserved to be captured by the cat lady, Kuki ends up coming to his rescue.

When Kuki hugs Wally in the end, he says "I love you," (as Mr. Huggykins) even though he didn't have to say it. (Note: This was what got me into Wally + Kuki ^^)

.DATE.
When Nigel tells everyone to split into couples, Wally and Kuki immediatly hold hands and have goofy smiles plastered on their faces.

At the party, they then proceed to the dance floor and start dancing. Very well, I might add.

.FAST-FOOD.
Wally starts worrying about Kuki and saying he shouldn't have let her go alone.

.GHOST.
When Kuki is being pulled into the grave (the second time) by the ghost hamsters, Wally is the first to run over and pull her out.

.BEACH.
The existance of this episode. Watch it and you shall understand. It's one of my favorite episodes. XD

.UNDERCOVER.
When they were all tied to an iceburg, Wally almost confesses his love to Kuki.

.END.
Wally pushed Kuki out of the way of the laserfire.

Kuki and Wally are right next to each other in nearly every scene.

Kuki saves Wally from falling when the platform starts to fall.

When Nigel says to brace themselves, Kuki and Wally hold onto each other.

Kuki was flirting with Wally when he was in space.

.LEADER.
When Lizzie told Wally to shut up, Kuki said, "Don't you tell Numbuh Four to shut up!"