Personal thank you's in email & DM. The personal touch goes a long way.
Also - you could have a batch of custom swag made up. Send it to them with a note explaining the exclusivity.
For instance - thousands of us have the standard grey Mailchimp T-shirt. What if they sent their top 1,000 users that shirt in red with a note explaining the "secret" that only the top users get the red shirt. It's relatively private but the user gets to feel like a rockstar.
Dan Pink teaches us that people value experiences over things, and specifically over money.
Send that person a $250 gift cert to share with their spouse/sig-other at one of the top restaurants in their town. For example.
If it is stuff, something creative. Shirts, smirts. We do that too but it's just another shirt.
We send things like a care-package with local Austin foods, a nice pint glass (with our logo, but tasteful) and things like that. Something memorable.
I like giving them "status" on the site or in the app. This is things like "Mayorships" in Foursquare or "Verified" on Twitter. The goal is to create a simple, exposed way that people can earn status. (This is similar to the "LinkedIn Connections game" that was played back in the day, you have to get to 500 connections but you don't want to be the person with their email address in their Name).
You want to be able to give them "superpower". See Kathy Sierra's Designing for a Badass User http://craftedresonance.quora.com/Kathy-Sierra-on-Designing-for-Badass
Something personal and/or something public. Recognition is inexpensive yet valued, so do something surprising which shows you appreciate them. Also, think about some other larger-scale activity like a meet up for drinks or something along those lines in a specific location. Even sending the invite is well received, even if they don't end up going. Plus, you get the chance to get live feedback and your customers can meet each other. Both good.