We did use an allowance system but it was for both of us and not just my wife. We pooled everything we earned and took out for all the budgeted living expenses - rent then later mortgage/taxes/insurance, grocery/household, car, vacations, etc. It was all done with a yearly budget in an envelope style system using Ing accounts to track it all with automatic withdrawals filling the accounts.
There were then three allowance accounts - mine, hers, and ours. The money in our allowance accounts could be spent on anything we wanted with no questions asked. The "ours" account was for us to spend on dinners out, concerts, etc.
Everything beyond that was saved though in the yearly budgeting process the max was always pre-allocated to the before tax accounts, ESPP if there was one, etc. Bonuses and stock grants weren't included in the planning and were always saved. Anything left over in the regular salary after the budgeted items was saved as well.