BTC-E charges 0.20% commission on each trade you make. So you buy coins they take 0.2%. You sell coins they take 0.20%. The fees for funding and withdrawal are different - they depend on the currency and payment method and can vary widely.
WRONG !
Why BTC-E still list PayPal on the list if they don't accept withdraw via PayPal ?
The fee for the withdraw is 5%. And the fee from PayPal to your VISA is 2 EUR / $2.50.
They only don't accept deposit with PayPal, because all the transactions are final. If a person deposit money with PayPal and buy coins, this person can file a fake complain to PayPal and tell them that the purchased coins aren't delivered and get the money back. That is the reason.
And I speak from my experience, I have a PayPal and a BTC-E account.