A friend recently showed me a pair of embroidered runners made by her aunt that had become yellowed with age. They had several pin-head sized dots of rust, but otherwise were still in really good shape. She was afraid to wash them and use them in her home.
My feeling has always been, "If you've got 'em, use 'em!"
Embroidered linens worked in cotton embroidery thread on cotton or linen grounds can be easily cleaned in room temperature water with a mild soap like Orvus paste or sodium borate (aka: Borax) dissolved in water with a ratio of 1 teaspoon per gallon.
Stubborn stains may need a longer soak, or spot-cleaning with an agent meant to work specifically on the type of stain. For example, small pin-head rust marks can be treated using a cotton swab dipped in a rust remover made for laundry use. Dab the swab directly on the stain and soak again. Rinse thoroughly several times in room temperature water, making sure all traces of the cleaner have been rinsed away.
Always avoid using bleach on your linens, as this can damage the fibers in older pieces, and always soak - never scrub.
The pieces can be dried flat on a cotton sheet, and for best results, press them while still damp to remove wrinkles. You can add a bit of sizing (starch) before pressing if you will be using the pieces right away, but if you are storing them, don't starch them as this can cause permanent creases when the starched fibers break along the folds.
This simple technique works beautifully on surface embroidered linens from the 40's and 50's - the ones most of us inherited from grandmothers or picked up at flea markets and estate sales.
This is by no means the only way, and different collectors and embroidery lovers have their favorite cleaning methods.
Elaborately embroidered pieces, historical treasures, items worked in silk threads or wool should be cleaned and restored by an expert, and delicate pieces should be conserved, rather than restored.