Both module types are used on this site.
The basic difference is that the Documents module is a straightforward file download listing. You upload, your users see a file listing which consists of filename, date, size, etc. and they can download the files. The Repository module allows the same functionality but it includes Summary and Description text where you can explain some details about the file, the listing is searchable and it allows your users to also rate and comment on the files. It allows you some flexibility in terms of the format as all output is template driven.
If you just want a simple, quick file listing, like on this site's downloads page, then the Documents module will do nicely. If you want to take advantage of some of the extra stuff like ratings, comments and descriptions, then try the Repository module. There's a User's Guide for the Repository module on the project's downloads page which gives you a nice overview of the module and how to configure it.
You could also use the UDT (User Defined Table) module which allows you to define some custom columns ( like the minimum version column on the downloads page here at dotnetnuke.com )
In the end, they'll all do what you want, it will most likely just end up being personal preference. :)
If you have any specific questions about the Repository module, feel free to post them in the Repository forum and I'll do what I can to help you out.