The 5430 satoshi limit. Is that to one individual?
Using the default configuration of the reference client, if any single output in the transaction is below the 5430 limit (regardless of what the total outputs are), then the entire transaction is considered "non-standard". The peer clients will refuse to relay the entire transaction, most miners will refuse to include the transaction in the blocks they are working on, and it will not show up in a wallet until it's included in a block.
If I send smaller amounts to many individuals like a faucet so that one transaction sends more than 5430 satoshi's but smaller amounts to many people, does that still work?
No. And even if it did, please don't. Instead, allow your users to build up stored value at your site until they reach at least 0.01 BTC. Then once a day you can create a a single transaction that will pay out to multiple users, paying each user who has accumulated more than 0.01 BTC. Better yet, allow each user to set the payout threshold for themselves, with the only requirement being that it must be higher than 0.01 BTC.
Do I have to pay a fee for each payment sent within the transaction? or only 0.00005btc for the entire thing.
The fee is 0.0001 BTC
per kilobyte or fraction thereof. How many kilobytes your transaction will be depends on several factors a few variables, but most significant is the number of inputs and outputs you are using. As a "rule of thumb", you'd probably be safe to assume about 185 bytes per input, 40 bytes per output, and about 50 bytes of overhead.
