So why is my wallet waiting for 3 comfirms on a small amount?
They wait for confirmations to ensure it can be successfully spend.
Also are there any guidelines wallet-software could/should follow for confirms?
No.
How does this work at the btc protocol? At which point can an output be used as an input ? After how many confirmations of the output ?
You can use an output even if transaction has no confirmations. There is no special rule. Wallets usually wait for few comfirmations to ensure it can be successfully spend.
The Bitcoins you receive may not reach your wallet if transaction is dropped later due to lack of fees or if there is a double spend(low chance). So the transaction you spend will be invalid. To ensure this won't happen, wallet usually wait for few confirmations.