I always reorganize it. One pet peeve of mine is when a program will install itself and put in multiple directories/links in the main start menu list.
Take Microsoft Office for example. It'll install links to all of its programs in the main list - making it much longer. But that isn't enough, Office will also install a directory for Microsoft Office tools. Now if you also want multiple versions (for example if you want Office Pro and Works Suite) then double the number of entries. Instead of having one huge @ss scrolling list, I make one Microsoft Office folder, and move all that junk into it.
However, I don't over do it. I won't make a programs folder, then a utilities folder inside the programs, then put the Microsoft Office inside the utilities. That would be a place for everything and well organized. Yet it'll take a half dozen clicks to do anything and the solution is worse than the original problem.
On a related note, don't you hate it when a program makes a separate directory with just one item in it? I'd rather just have that one item!