Compared to Slush's pool, how exactly does Eligius payout owed bitcoins to the miners? 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?
How does Eligius pay miners directly from the newly generated coins?


It simply generates the coinbase transaction to include payments directly to its miners, instead of only a transaction to itself.


  What are the pros and cons of this compared to how Slush does it?


Here are some I can think of:

Pros:


No transaction fees necessary for these payouts (except for the opportunity cost of some transactions you're not including in the block; but unless the block is at the max size, this is 0 cost)
Some people like having freshly minted coins, for anonymity and just because it's cool


Cons:


Harder to predict when you'll get a payout (because you have to wait for the pool to find a block)
If you're far down the queue, it might take several blocks and/or a manual payout before you finally get your payment



  Are there other pools that do the same thing?


Yes, at least a few. BitPenny and P2Pool, for instance.


  Is this only possible with BTC and it's clones or can Litecoin pools do it too?


It's possible with any Bitcoin-like coin, including Litecoin.