I had the opportunity to borrow some episodes that a friend taped when they were first run. Thus I was able to compare them with the syndicated versions I have taped.
In most of them, the beginning monologue or comedy bit has been cut for syndication. The story doesn't suffer by having them out. An example is an opening scene with Kramer and Newman on a park bench discussing the Bermuda Triangle and alien autopsies. It's not part of the story, though it is very funny. These are the things that are usually cut to make room for more commercials, as well as Jerry's stand-up routines. However, there was one episode (The Foundation) that was intriguing. The beginning and end - the visit to Susan's gravesite, and Elaine's subway ride with the men discussing the urban sombrero - were integral to the story and were not cut. Thus I ran the original and syndicated version side by side and was able to see where the cuts were.
In many scenes, a second here and there were trimmed (where there is no dialogue). Part of a sentence of George's at Susan's grave is cut - can't be more than a millisecond! And part of the scene showing Jerry standing with Susan's parents. They cut Mrs. Ross offering her flask to Jerry. In syndication they only show him refusing it. Then at Jerry's apartment, they cut the first few lines spoken by Jerry and George; they are talking about the funeral, and Jerry is taking off his jacket. In syndication the scene opens with his jacket already off.
Part of Peterman's dialogue at the meeting table is cut - a scene where he drops apples and pears on the floor which indicates that he is suffering burnout and explains why he later goes to Burma and puts Elaine in charge of the company. In the syndicated version the order of Elaine's dialogue is shuffled in one part
Most of the missing parts are not integral to the story, yet the one scene with Peterman was important to understand his breakdown so I think that explains why certain episodes seem incomplete - little things were cut out that would explain the plot development a little better. I don't have access to all the first-run episodes though - just a few that my friend happened to tape and save.
So those of you who do have the originals on tape - you've got a more complete story there. I have only the ninth season originals and of course the few that my friend taped.