The RPC interface certainly is not the fastest. There is a C++ blockchain parser that someone wrote that you could base your system on. If you want a really simple and quick solution that depends on a central server: use blockchain.info's api. It can be queried for all txs regarding a certain address.
On another node I wrote a python script to parse through all txs in all blocks, does some calculations and stores everything back into a database - it takes a while but works fast enough. The biggest hurdle for me was that I ran out of network sockets since somehow bitcoin-qt or my python rpc interface never closed them - so I had to tweak some parameters of linux network stack. Other than that look ups and writes to my database were much slower than the RPC interface.
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As far as I'm aware virtually all exchanges have written their own Bitcoin implementations, at least to some extent. It's a complex task. If all you're doing is looking for payments to your addresses, you could try writing an app using bitcoinj instead which may be a higher performance way to get what you want (connect it to a bitcoind you control, obviously). You will also need to handle re-org events and other tricky things.
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