multi wallet bitcoin client
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