There are two types of EWallets, hosted (shared) EWallets and hybrid EWallets.
With hosted EWallets, all the coins are shared (all customers funds are combined) in the host's EWallet. Examples of this are Paytunia.com, Instawallet.org, EasyWallet.org, WalletBit.com, as well as the online wallets with the exchanges, such as MtGox.com, Bitfloor, etc.
With a hybrid EWallet, the private keys are kept locally but transactions route through the EWallet provider. To protect from loss, the browser-based hybrid wallets store an encrypted copy of the data from the wallet online with the EWallet provider. The provider doesn't have the password to decrypt the wallet stored with them and thus has no potential to spend your coins stored with them.
So your risk of fractional reserve exists only with the hosted EWallet providers.
One method these providers could prove they are not a fractional reserve would be to submit to sporadic financial audits. None do this today.
Another option would be for the EWallet provider to treat each account as if it were a standalone wallet. That way the blockchain would verify that the coins received have not been spent. No EWallets operate this way either.
When multisignature becomes functional, this will likely be a security feature available from one or more EWallet providers.