Similar to this question, How can a website detect when bitcoins have been deposited?, is there a way to accept altcoin deposits on a website and have the website automatically know when the altcoins have been sent to the website and update the user's balance accordingly? Is there a procedure common to all altcoins or does each altcoin need a completely different approach?
Most (99%) altcoins are just Bitcoin clones, so the same process applies, you just need to use the appropriate daemon (dogecoind, litecoind, etc). If you need extra help, we'd need to know which altcoin. In addition depending on how popular the altcoin is there may be the equivalent of Blockchain.info (has merchant services for Bitcoin), eg. DogeAPI.