Hi,
actually starting from Quartus II v9.1 the ptf file won't be generated as I know. Instead a new xml file ".sopcinfo" will be generated which specifies how the system is constructed.
The following package is a prebuilt NEEK system which I used to run uClinux on:
http://www.nioswiki.com/@api/deki/files/115/=neek_ocm_spi.zip (source:
http://www.nioswiki.com/operatingsystems/uclinux/mmcsd)
I can also recommend you to go through the NEEK system architecture tutorial:
http://www.nioswiki.com/nios_ii_system_architect_design_tutorial?gsa_pos=1&wt.oss_r=1&wt.oss=nios%20architecture which could give you a good starting point for developing own SoPC Builder systems for NEEK.
Cheers,
D.