The answer depends on the context of the question. Let's say for example you're shopping for a hard drive on newegg.com, and you see two Maxtor 80 Gig HD's that have the same specs, only one says "Retail" and costs $125, and the other says "OEM," and costs $117. Well, they are both going to be indetical hard drives...the retail version will come in the pretty retail packaging. It will usually include some stuff like cabling, instructions, and maybe software, whereas the OEM version pretty comes in a plain white box (if it's even in a box at all) and won't have most of the extras. If newegg buys OEM hard-drives for resale, they will come in one big box that has, say, twenty hard drives in it, whereas the retail product comes individually packaged for display.
Now, in terms of your question about "third party" manufacturers, again there is a context to consider. Let's assume you're talking about graphics cards. ATI makes their Radeon processor, and then designs a reference board which shows how the card should be assembled, indicates cooling requirements, etc., and what kinds of discreet components are required to make the whole thing work. Now, ATI mass-produces their own cards, and all of them adhere fully to their reference design, which should be obvious. However, companies like Sapphire and Visiontek also produce ATI Radeon cards, and they might choose to deviate ever-so-slightly from ATI's reference design, for whatever reason. They may want to decrease the cost of producing the cards by using cheaper (slower) memory, or they may want to improve the cooling solution to make it more overclocker friendly...whatever the reason, the third-party still must maintain a level of quality as dictated to them by ATI, but they also have a bit of leeway to adapt the product to their own specs.
It's impossible to give you one answer as to how a third -party product differs from a reference design; you have to do research on a case-by-case basis. Sometimes, the third-party product actually ends up being superior to a reference design, so you really have to check it out by researching benchmarks, looking at product specs, and determining the truth for each specific product.
Those who live in glass houses shouldn't take showers. :tongue: