I have mined a bit on both pools. Slush builds up an amount in your account and once it passes a threshold that you set, Slush sends you a payout that comes from another wallet. Eligius sets the threshold (and it is quite low too), and once your "account" passes it, Eligius sends out the payment directly from the newly generated coins.
I have enough imagination to see how Slush's pool and site manage the workers and send out the payments, but I cannot wrap my head around how Eligius does it that way.
How does Eligius pay miners directly from the newly generated coins? What are the pros and cons of this compared to how Slush does it? Are there other pools that do the same thing? Is this only possible with BTC and it's clones or can Litecoin pools do it too?