multi wallet bitcoin client I'm looking for a bitcoin client capable of handling multiple wallets. At the moment I'm developing a shop which will allow bitcoin payments. The idea is to create a new address for each client making a transaction.

So what client should I use? I'm going to use Debian (possibly Ubuntu) server. Hopefully it will not require lots of resources (at the moment ~1GB of ram is max I can give but ~512MB is preferable).

Also I would like the solution to scale well. So perhaps working with wallets is not a correct thing in the first place? For example should I work with raw transactions ("send from temporary address X to the main addres A") instead? And only synchronize the main wallet?
You can use electrum and create a dedicated wallet for your shop's transactions using this command:

electrum -w shopwallet -f 0.0001 -G 100 create

This will create a new wallet with a gap limit of 100 i.e. it will track 100 addresses by default (more will be tracked as you start receiving payments).

Once you have the wallet setup you can get the master public key (MPK) via the wallets menu > master public key. You can install the MPK on your web server allowing you to generate receiving addresses for your customers without risking your coins.

Two example implementations of this approach are:

Bitcoin payments for Woocommerce: http://wordpress.org/plugins/bitcoin-payments-for-woocommerce/

Stick's address generation scripts: https://github.com/prusnak/addrgen