+1 This is useful when the folder is written by some programs which writes temporary. Having an option of letting the files 'settles' before syncing would help a lot. The best would be able to apply this to subdirectories selectively.
+1 I think having .sync/IgnoreList as a machine specific and .syncignore as global setting (can be put into any folder). This will be same as Git and I believe it is the most logical and powerful solution.