Cyclone3-Overshoot/Undershoot

The RAM signals look quiet good, compared to some waveforms shown in Altera applications note. If they verify in real life, I would be happy. With terminated SSTL I/O standards you should mainly think about correct RAM operation rather than exceeding maximum ratings.

The LVDS waveforms may not endanger the CIII parts (most likely), but they show incorrect levels anyway. You seem to have forgotten the 100 ohm terminating resistors at the receiver. A correct lvDS signal has a much lower voltage variation, around a common mode level of about 1.2V. With termination resistors, the overshoot will be gone.