Windows only: FreeFileSync has a myriad of options for syncing files between two folders and locations. The user interface is especially user friendly and makes it easy to quickly adjust your settings.
Whether you need to simply compare to folders and update the files to the newest version or you want to create batch files for recurrent comparisons, FreeFileSync has you covered. If you have multiple locations to compare, you've saved a document to My Documents, on a flash drive, and have an emailed copy of it you just downloaded, FreeFileSync can compare all three versions easily.
You can specify whether you want file comparison to be based on size and date or you can have it do an actual comparison of the file. You can quickly switch between simply comparing and actually syncing the files, when you're ready to sync the central column between the two comparison panes allows you to rapidly choose which file will get synced in which direction or which files should be temporarily ignored by the syncing process.
If you're not tweaking things manually with the centre column you can sync everything bit for bit with a mirror sync, use the two-way sync to copy the new files from the each folder to the other folder, and the update sync where only the new and updated files will be copied.
Have a favourite file syncing tool? Share it in the comments. FreeFileSync is freeware, Windows only.