Design analyse methods

Dear Sir or Madam,

when tyring a complex FGPA design on real hardware 
what possibilities do exist to analyse the design ?
Of course one possibility are debug pins but the problem
is that their availableness is not always given.

Simulation might be a good first step in order to prove
first correct functionality but what if there are
some components which cannot be reproduced my models so
easily? 
Are their any tools (for Altera Cyclone FPGA) which allow
to observe the diffent signals live (not simulation!) without having
to route them to output pins (which are of limited number anyway,
apart from that
the timimg may be changed in an unmeant way) ?

Thank you for your information and help.

Best regards

Andre