I am looking for a money management / financial advisor software to help me to decide:

1. which retirement account (sepIRA vs self-employed 401K) to open,
2. which expenses are tax deductible
3. how to decrease my taxable income, etc.

I've looked at Quicken and Microsoft Money, but the vast majority of features in their software packages are useless to me. For example, they offer budgeting, bill paying, and checkbook balancing features that I already get with my online bank.

Do you know of any good financial advisor software programs for a self-employed business owner like myself?

It sounds like you'd be better off talking with a CPA than looking for a commercial software package. Tax preparation software will help with items 2 and 3 but cannot replace working with an actual person.