What is the best way to merge thousands of duplicate leads without Marketo services?

There is no free way to do this.

Some tools:
-Intern
-Demand Tools
-Marketo Merge Service
-RingLead

Best thing to do is a big cleanup, and fix your processes to prevent dupes. See
http://www.marketingrockstarguides.com/six-principles-data-cleanliness-1566/

Cloudingo +1

You can subscribe to this tool, which integrates directly to Salesforce, for an entire year, for the price of a one-off a Merge Service project from Marketo (not that Marketo's Merge Service is a bad option either! I've used them once for a big merge project and they did a great job as well.  Just sayin'...if you need lots of de-duping, Cloudingo is probably the most cost-effective way to go. Not to mention you can set up automated rules to sweep for and merge duplicates on an ongoing basis, so you can basically set it up and forget about it. =D )

http://www.cloudingo.com/pricing

I don't think you'll find a total free service that does that.

I am from TIBCO team. I would like to introduce TIBCO Clarity.

You can try TIBCO Clarity for free.clarity.cloud.tibco.com/landing/index.html

It has a really powerful and robust de-duplication function.

You can customize your match strategies by columns or by swappable columns or by columns against to a thesaurus table, and then use them to discover duplicate records from any incomplete or partially similar records, even from records in different languages.

In addition, It has deep integration with both Salesforce and Marketo. It can help you directly update and remove duplication data in your salesforce and Marketo account.