I know that
multibit has the capacity to have multiple wallets, but no API access.
bitcoind has great API access, but only one wallet. Is there any solution that combines the two?
QOINPro is an online wallet for around 10 cryptocurrencies including Bitcoin, Litecoin and Dogecoin. Additionally, they award coins daily just for being signed up. It's not much, but something while they don't charge anything.
The wallet that I develop, Coinomi, has a core library (java based) that could be used to host 9 cryptocurrencies at the moment. The private keys are always stored on the client and not on the Electrum servers that it uses to update it's state.
Currently you need to include it in your java project but it is possible to create a JSON API to be language agnostic, it just needs some development.