I have heard stories that the Eurocontrol computer will throw a flight plan out if your equipment doesn't meet the minimum route requirement, particularly mode-S.
The only equipment list issue I know of which CFMU will chuck a flight out for is not declaring 8.33 if filing at FL200+. I've tested this and it does indeed happen.
Maybe it chucks out some RVSM-airspace stuff too but that comes in a lot higher up.
The one bizzare thing which I did recently get was some "overly diligent" operative at homebriefing.com who amended my filed route (which was NOT marked "ifps reroute accepted) from FL100 to FL090 because I filed (as I always do) S/S and thus did not declare BRNAV carriage which is mandatory at FL100+. So now I always file SYRG/S
I am not sure that SG/S would be enough, because while GPS is the only means of GA compliance with BRNAV, it is actually the BRNAV bit (R) which matters in the legal equipment-carriage sense. A suitably approved KNS80 would actually meet BRNAV too legally (though not usefully).