Typically when you are talking about probate matters such as an inventory of probate assets those assets which pass by contract (such as the joint account or TOD accounts you cite, as well as life insurance or annuities with named beneficiaries) are by definition not included in the inventory as "non-probate" assets. Keep in mind however for most transfer tax purposes they are included. You should however have the advice of counsel in the state where this matter is taking place.
Joint account: Not listed on a probate inventory, but listed in an estate tax return.
Stocks: Use value as close as can be determined to date of death value (try using the stock quotes from the Globe or Times for that day).
If a bank account is owned as JTWROS part or all of the date of death balance will be included in the gross estate for federal estate tax purposes depending on the identity of the joint owner. If the joint owner is a surviving spouse, only 50% is included. If, however, the joint owner is someone else 100% is includible unless the estate can prove that some percentage was contributed by the survivor. If the account is held as tenants in common (without survivorship rights) only the decedent's proportional share is includible.
An account that is TOD is 100% includible in the owner's gross estate.
My understanding is that MA has decoupled its estate tax from the federal tax and it is now a stand alone. Check with local counsel as to whether the result is different at the state level.
You probably want to have an attorney assist you in carrying out your duties as personal representative. Some items are included in the person's "taxable estate" for IRS purposes and not included in the person's probate estate for state probate purposes. As the others have said, you would include 50% or 100% of a joint account, depending on the facts, and you want to use stock values as close to the date of death as possible.