I do certain things to keep my inventory clean:

1) Do not keep basic mats that are needed to be crafted into something else like for example fleece. Directly use them to craft the items you will really need.
2) Check prices regularly. Doesn't make sense to store items you can buy at vendors or very cheap at the market place
3) Do not store too much stacks of the same item. Rather sell a stack or use a stack for crafting.
4) Know what your DOH needs in masses (for leves or mass synthesis) and concentrate on these mats.
5) If you aim to craft each item at least once, get the exact number of mats you need and try not to get more because it will flood your inventory too quickly
6) Regularly check your inventory and retainers for obsolete mats and compare your retainers for double-ends