What EURO exchanges have web APIs currently? I'm wondering what exchanges in that operate in native euro, who most likely support sepa transactions have web apis? 

Bitcoin-24.com was great until they had banking problems. now who is left? Is BTCe the only one?
There are quite a few exchanges in Europe with APIs. Use the Bitdango exchange search to find exchanges in European countries:

http://bitdango.com/exchanges?countries=BG,CZ,DE,FI,FR,GB,HR,MT,NL,NO,PL,SE,SI

Or use the Bitdango market search to find markets that use Euros as quote currency:

http://bitdango.com/markets?quoteCurrencies=EUR