You can modify a number of settings for reports and graphs on the Advanced tab. (Not all options are available for every type of report or graph.)

Amounts

Include unrealized gains

Tax-related transactions only

Transaction types

Status

Transfers

Subcategories (income and expense or budget reports and graphs only)

Categories (budget reports and graphs only)

Show me change alerts for this report

Tax form (only in Quicken Business & Personal)

Report Basis (only in Quicken Business & Personal)