In the Finder theres a command "Clean up", which can be used to position the icons of a Finder window (in Icon view) in a regular grid. But the distance between the icons is very large under Mac OS X, much larger than under classic MacOS. Under Mac OS X 10.3 (Panther) the distance is even larger than under Mac OS X 10.2 (Jaguar), which makes this feature often almost useless because of the waste of space.
The application Tidy will solve these problems. Tidy will also tidy up the icons, like the Finder, but it is much more powerful. With Tidy you can configure the horizontal and vertical distance between the icons in a wide range. Also there are several different grids, you can select how many columns of icons will be used. You can even move all sub folders to the top followed by all other icons, so all folder can be reached more easily (no more searching for a certain folder which is burried in tons of other files).