Since this topic is being discussed, I will plug my own tools,
SQL Exec Stats
and (a little dated) documentation
the main capability is cross-referencing index usuage with specific execution plans.
another feature is generating execution plans for all stored procedures in a database, along with the index usage cross-reference.
There are several sources of execution plans or plan handles,
this could be a live trace, a previously saved trace, previously saved sqlplan files,
from dm_exec_cached_plans, dm_exec_query_stats, etc
from SQL via SET SHOWPLAN_XML etc
all are useful, so we need tools to make use of execution plans from all sources
I could also mention my own performance monitoring tool, which needs to be updated or incorporated into a commercial tool,
the point of note is that is shows disk IO from performance counters, and from fn_virtualfilestats with the data, log and temp read/write all simultaneously
Finally, there is SQL Clone, which started in SQL Server 2000, but in SQL Server 2005 and later, we have the API to get and update data distribution statistics.