1. Establish version retention setting sooner rather than later – it’s because having versioning turned on not only provides a safety net in the event that a corrupted version gets saved but also because you’re able to track changes (and see who made them) from version to version at a glance. set the number of versions such that you Optionally limit the number of versions to retain to three - it's because turning major versioning on for your library means that you can eat up server space quickly (copies of entire documents are saved), and three seems to be a reasonable number, unless otherwise special requirement.
2. Keep the number of items in a library under 2000. Throughput performance degrades as the number of documents increases when flat library storage is used. SharePoint can't store more than 2000 documents per folder.
3. Use folders over filtered views because folders are twice as fast at bringing up a list of documents as opposed to filtered views of a larger list.
4. Larger lists are broken down into multiple document libraries. In many instances, large lists of documents can be divided into logical groupings that can be placed in individual document libraries. This would improve performance
5. Pervasive use of folders in a document library is not either helpful or desirable. While an occasional use of folders might help categorize documents, folders are really just a way to apply metadata to a document without having to create a column in the library.
6. If large libraries cannot be avoided then try to use folders. Use the search functionality to display these items. This will avoid queries and will utilize SharePoint’s search which is indexed.
7. In libraries that have versioning enabled, the storage used for previous versions counts towards the site quota. Be aware of this fact and plan accordingly.
8. Do not keep archive libraries or lists.
9. If there is a collection of large files that end-users often access, and if these files are updated infrequently, you should store them outside Office SharePoint Server. Instead, consider using an offline collaboration client.