Hi, I would recommend you two systems OtO and Lance.  You can find information below:

1. http://link.springer.com/chapter/10.1007%2F978-3-642-31095-9_19

2. http://www.ics.forth.gr/isl/lance/

As you are primarily interested in matching on instance level, you might also be interested in record linkage or entity resolution approaches. See the following link for instance:

http://infolab.stanford.edu/serf/#soft

There is a trick that makes an instance just a special version of a relation. Define a class Singleton  and define it such that for every Class A there is a unique non trivial relation to Singleton. Then trade an instance a in A for a non trivial relation from Singleton  to  A.   

Dear Sebastian,

I recommend you visit the following website :

 http://islab.di.unimi.it/im_oaei_2015/index.html

It summarizes the detailed descriptions on the results of different instance matching systems who participated in OAEI 2015 campaign.

http://islab.di.unimi.it/im_oaei_2015/index.html

http://oaei.ontologymatching.org/2015/results/index.html