Good point, Pat. I'll think of your question in terms of the holes at the time of construction. Since I know Flynn best and classic courses better than modern ones, I'll stick to my area of relative expertise.
There seemed to be two schools of thought in designing par 5 holes, either unreachable in two or reachable. Crump and Hugh Wilson liked their par 5s as unreachable in two and only had two at par 5 holes at Merion and Pine Valley (Flynn only had 2 at Lehigh). Crump's 7th and 15th holes at Pine Valley and Wilson's 2nd and 4th holes at Merion were very long in their day and remain so today. The 2nd at Merion was lengthened by Flynn prior to the 1934 US Open to keep it a genuine 3-shotter. Unlike the others mentioned, it is not a 3-shotter for everyone but remains so for nearly everyone.
Flynn made some sure 3-shot holes such as the 9th at Rolling Green (which I doubt anyone can reach even today in two shots at 625 yards from the tipsbecause of slope and elevation change), 16th at Shinnecock Hills, 17th at Boca Raton South, 9th at Boca Raton North, 5th at Cascades, 6th at Mill Road Farm, 3rd at Philadelphia Country etc. but he also designed par 5s reachable in two such as the 7th and 17th at Rolling Green, the 6th at Philadelphia Country Club, 18th at Kittansett, 2nd at TCC-Pepper Pike, 8th and 14th at Mill Road Farm (later changed to par 4s).
I think Flynn built wonderful par 5s, long and short. It is probably hardest to design a great long par 5. The 9th at Rolling Green is an excellent example of a great really long par 5. I don't think there are many, but the Merion and Pine Valley par 5s are definitely included in a list of great long par 5s.