FMC vs interlaken

You can't really compare FMC and Interlaken. There isn't anything the same about them - except, perhaps, they're both aimed at supporting higher bit rates.

FMC is Altera's name for a type of physical connector that they (and others) use. Interlaken is a protocol that you might run over a physical link that may (or may not) run over an FMC connector.

Have a read of:

http://www.altera.com/technology/high_speed/protocols/interlaken/pro-interlaken.html (http://www.altera.com/technology/high_speed/protocols/interlaken/pro-interlaken.html)

to give you an overview of Interlaken.

Altera's FMC is a custom connector made by Samtec, part number: ASP-134486-01

http://www.samtec.com/documents/webfiles/cpdf/asp-134486-01-mkt.pdf (http://www.samtec.com/documents/webfiles/cpdf/asp-134486-01-mkt.pdf)

This connector is used on a number of Altera's development boards.