1) if an outdated client receives a transaction with an unknown version, it invalidates this transaction?
Transactions with unknown versions are assumed to comply with the most recent transaction rules.
The only type of transactions so far are version 1.
For blocks, there are 3 types so far.
Version 1: Default
Version 2: Coinbase contains block height
Version 3: Signature encoding (BIP 66)
Version 4+: ?
?
??
Version 1 blocks will be rejected by the network since the 95% rule was met for version 2 blocks.
If you have a block with version 10, it has to follow all the rules for version 2 (include the block height).
Version 3 blocks don't get any special rule at the moment. Once 75% of the miners update, then version 3 (and higher) blocks will have to follow the BIP 66 rules.
2) what happens if 99.99% of the network already uses the new version and mine is outdated?
Transactions don't become outdated. New clients will be able to handle old transactions (or at least they should).
It wouldn't be fair if you lost bitcoins because you created a transactions and then when you tried to submit it, it was out-dated.
3) there is a website where I can see the percentage of version 3 blocks on the network?
This graph shows the acceptance. Not sure how often it is updated.
