The first place to look would be the execution plans for your long running queries. From there you can figure out the indexes which need to be adjusted or created so that the queries will speed up. If you have all the indexes in place this white paper will explain what database maintenance needs to be setup and why.

Once all tables are properly tuned you may need to update your statistics if you aren't doing that already.

Next check your RAM configuration to make sure that you have enough RAM to hold the data in the buffer cache that you need. If your buffer hit ratio is to low you may need more RAM.

After that you may need to look at your storage subsystem to ensure that it is powerfull enough.

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