If you are not creating Gift Certificates to use with your E-junkie store, then it's really easy. You just create a product whose price is the amount of the certificate, and post that product's button codes to your site. You would still need some way to provide "proof of purchase" that can't be forged or duplicated; in this case, we would recommend using either the Send Stored Codes or the Send Generated Codes settings to track "serial numbers" for the certificates you sell.
If you Send Stored Codes, you would pre-generate a list of codes (aka keys) and paste that list into the gift cert. product's configs where indicated; we issue one code from the list per product unit ordered until the list is depleted, and we notify you when the list is down to your last 5 codes, so you can replenish the list.
If you Send Generated Codes, it saves you the trouble of pre-generating keys and periodically replenishing that list, but it takes a bit more up-front work to setup. When configuring your gift cert. product(s), you provide your Code Generator URL that outputs a unique code every time that URL hit (i.e., when you browse to it, you see nothing but a unique code every time). We simply take the raw text output of that URL for each purchase and paste that text into the buyer's thank-you page and thank-you email (and also into your sales-notification emails). In this case, you would be solely responsible for finding a Web service that offers this type of URL, or otherwise for installing and configuring your own programming script to respond at that URL -- we only hit it for some output and pass whatever it gives us along to you and the buyer.
Whether you pre-generate a list of gift cert. keys or have the keys generated on-the-fly with each purchase, you could maintain a master list of purchased codes at your shop. When someone comes in to redeem their gift cert., you would match the code they provide with your master list and, say, cross off that code so any duplicate would not be redeemable.
If you want to get really fancy, you can configure the gift cert. product to offer a File Download of a generic certificate image, where buyers could print that out and write the code from their email on the printed certificate.