Material Issue is generally made for the low value consumable items like office stationary, product consumables etc. Also you can create Material Issue to reconcile serialized and batched item's stock.
Material Receipt entry is created to inward stock of item(s) in a warehouse. This type of stock entry can be created for updating opening balance of serialized and batched item. Also items purchased without Purchase Order can be inwarded from Material Receipt entry.
In the manufacturing process, raw-materials are issued from the stores to the production department (generally WIP warehouse). This Material Transfer entry is created from Production Order. Items in this entry are fetched from the BOM of production Item, as selected in Production Order.
Manufacture is created from Production Order. In this entry, both raw-material item as well as production item are fetched from the BOM, selected in the Production Order. For the raw-material items, only Source Warehouse (generally WIP warehouse) is mentioned. For the production item, only target warehouse as mentioned in the Production Order is updated. On submission, stock of raw-material items are deducted from Source Warehouse, which indicates that raw-material items were consumed in the manufacturing process. Production Item is added to the Target Warehouse marking the completion of production cycle.
Repack Entry is created when items purchases in bulk is repacked under smaller packs. 
Subcontracting transaction involves company transfer raw-material items to the sub-contractors warehouse. This requires adding a warehouse for the sub-contractor as well. Sub-contract entry transfers stock from the companies warehouse to the sub-contractors warehouse..
