<ol>
<li>What are the patterns you use to determine the frequent queries?    </li>
<li>How do you select the optimization factors?</li>
<li>What are the types of changes one can make?</li>
</ol>

Your question is a bit vague. Which DB platform?
If we are talking about SQL Server:
Use the Dynamic Management Views. Use SQL Profiler. Install the SP2 and the performance dashboard reports.
After determining the most costly queries (i.e. number of times run x cost one one query), examine their execution plans, and look at the sizes of the tables involved, and whether they are predominately Read or Write, or a mixture of both.
If the system is under your full control (apps. and DB) you can often re-write queries that are badly formed (quite a common occurrance), such as deep correlated sub-queries which can often be re-written as derived table joins with a little thought. Otherwise, you options are to create covering non-clustered indexes and ensure that statistics are kept up to date.