I think you should have a mixture of pre-tax and after-tax accounts, like a regular investment account and an IRA or 401(k) plan.
The IRA and 401(k) plans are great because of the tax benefits, but if you have a financial emergency, you pay a 10% penalty in many cases if you take money out of an IRA or a 401(k) plan before you are 59 1/2.
On the third hand ;-), if your employer allows a loan to be taken against the 401(k) plan, then you can just borrow the money and pay it back to yourself. But you can't borrow against an IRA. :(
Oh, whatever you do, don't have too much cash in a savings account...the interest rates are terrible!