Deduping Tools
See Duplicate Management for standard Salesforce Deduping. Use that unless you have specific needs.
Other Apps
Duplicate Check for Salesforce
https://appexchange.salesforce.com/listingDetail?listingId=a0N300000055fXxEAI
free for first 10,000 rows.
Batch and automated in paid plans
Also merges up to 15 account.
May be good for a first cut bulk merge.
See pricing http://www.addressedworld.com/pricing/duplicate-check-for-salesforce
Reasonably priced, good features.
EXCEPT, you can't dedupe custom objects without the Enterprise Plan for $1299 / year
Is number of records the number of records in your system available to be de-duped or the number of de-dupes performed?
Dupe Blocker
Dupe Blocker and Demand Tools for NFPs
Download the trial of Demand Tools (http://www.crmfusion.com/demandtools/), and then send CRM Fusion an email (nfp@crmfusion.com) asking to get the free NFP licensing for both Demand Tools and Dupe Blocker. (see http://www.crmfusion.com/nfp.php). You need to include your OrgID and your NFP confirmation (eg a copy of your DGR status or the ATO certificate is fine).
Free for NFP's so it is great!
Really good tool
However
You need to keep on top of the indexing - especially after a large import.
Dupe Catcher
Free - so until the SF one comes out then this one may be good enough - but push for a real dupe blocking tool like Ring Lead.
Other Apps
Live Services
Work as you are editing the record.
Cloud services
Ring Lead http://www.ringlead.com/salesforce-applications/data-cleanse/
Cloundingo