Episodes suggesting a friendship
In Take the Plunge: Part 1, Eraser and Pen agree with each other that they are cool.
In Barriers and Pitfalls, Pen and Eraser go together to find Blocky.
In Are You Smarter Than a Snowball?, Pen and Eraser are happy to see Blocky with the test answers.
In Sweet Tooth, Pen helps Eraser out by having $8 and finding a $1.99 dollar on the ground, so that both of them can buy Leafy's cake. However, 9.99$ wasn't enough, so Eraser thinks up an idea to take Coiny for Leafy, because he's a penny.
In Bridge Crossing, Eraser asks Pen for a third bridge when both bridges are broken.
In Cycle of Life, Pen is happy when Eraser carries him.
In Don't Lose Your Marbles, Pen and Eraser are seen standing next to each other.
In Vomitaco, Pen says "Which is?" for Eraser, because Eraser has been eliminated.
In Return of the Hang Glider, Pen and Eraser are seen talking to each other in the beginning.
In Getting Teardrop to Talk, the episodes starts with Pen showing Eraser a "Rectangle" which is actually a parallelogram, as corrected by Eraser. Pen then brings out a Pentagon, causing Eraser to freak out. Pen later tries to get him along with Eraser and Blocky to stick together. Eraser hears "Free Food" and leaves.
Episodes suggesting a conflict
In Insectophobe's Nightmare, Eraser doesn't seem concerned Pen is getting hurt while doing the six-legged race.
In Bridge Crossing, Eraser also destroys the "ropes" (actually black bendy straws stuck together with tape) while Pen is getting across, though it was an accident.
In Half a Loaf Is Better Than None, Eraser gets mad at Pen for saying his line/catchphrase "Which is?".