TJC wrote:
<<If I were to start a self-directed Roth IRA through a discount broker (such as Waterhouse), do I pay commissions on transactions just as if I were buying and selling regular securities, or does it depend on the broker? Also, is it possible to set-up an automatic investment into the IRA, for example, have my broker invest according to my preset instructions once a month into the IRA?>>

See TMFPixy's earlier post regarding commissions. Waterhouse will let you set up a periodic investment (monthly or quarterly) for any mutual fund they offer with no transaction fees (approx. 800 funds). The minimum is $100. However, any commissionable trade has to be initiated by the account holder (or someone with power of attorney).