Haven't given it much thought but here are a couple of ideas:

1) Users pay to list their domains.

  Pro: Guaranteed revenue from every user
  Con: Low motivation for user to pay up as there's no guarantee for reward

2) List up to 20 domains for free anything over that falls into a tiered annual payment plan

  Pro: same as 1 but better because of larger free user base who might be more likely to convert to a paying user
  Con: Could a user just keep rotating hundreds of domains through their free account? (imposing a limit on how many times a user can list and de-list domains would prevent this)

3) Users pay a flat fee only when a successful trade is made

  Pro: more motivation for users to pay up as the reward is imminent. Also both users can split the fee making it more affordable for each of them
  Con: Revenue is conditional on successful trades. Could the users use the service to simply list their domains then use outside channels to complete the actual trade/transaction?

4) User pays a fee when they want to take a domain they received through trading off of the trading block. This would require the site to actually assume ownership of all domains being traded then hold them hostage for a small fee when a trader wants to take possession of them (or else they are still up for trade/in limbo)

5) Maybe the site handles trades as well as cash purchases. Trades are free.. purchases incur a 2% fee.

6) Ads for other internet services. Perhaps the domains could be contextually paired with the ads so that if a user is searching for mma-website.com he/she sees ads for mma training equipment and facilities.