I would use the first one or a variant of the last one. The second one isn’t correct. There are some nuances, too.

In the first one:

Douze euros ? À peine de quoi rentrer dans mes frais.

The construction breaks down as

Rentrer dans mes frais (~ pay for my expenses, though not quite)

De quoi rentrer dans mes frais (= enough to pay for my expenses)

À peine de quoi rentrer dans mes frais (= barely enough to pay for my expenses)

An implicit "C’est" is to be understood as preceding "À peine". It’s something that the speaker can either say to the person who just paid them (in complaint), or say to themselves, or say to a third party.

The third one would need to be adapted a bit, because the subject of "rentrer dans mes frais" needs to be "je", rather than the twelve euros. You wouldn’t say "Douze euros rentrent dans mes frais"* to indicate that twelve euros pay for your expenses, you would say something like "Avec douze euros, je rentre dans mes frais". With that said, a construction like the following would work:

Douze euros ? Ce qui me permet à peine de rentrer dans mes frais.

The construction breaks down as

Rentrer dans mes frais (~ pay for my expenses)

Me permet de rentrer dans mes frais (= enables me to pay for my expenses)

Me permet à peine de rentrer dans mes frais (= barely enables me to pay for my expenses)

Ce qui me permet à peine de rentrer dans mes frais (= which barely enables me to pay for my expenses)

This is a complementary clause qualifying the twelve euros. To me it doesn’t sound as much like a complaint as the first one. I would imagine it only be used to describe the amount after the fact, either to oneself, or to a third party; if said to the payer, it would sound to me like an observation rather than a challenge.

As for the second one, "À peine ce qui" isn’t idiomatic — only "À peine de quoi".