Why do you ask? Is it because you're finding low rates at those sites?

In those cases, you should look into the various hotel programs' Best Rate Guarantee (BRG) features. At Marriott (where it's called Look No Further or LNF for short), you get a room rate 25% below the third-party rate you found (and for any number of nights, and for no limit on how many nights or stays per month), and you get to earn points and status qualifying nights, so that's even better than booking on the third-party site, isn't it?

http://www.flyertalk.com/forum/marri...rsion-brg.html

At several other programs, you get your first night free if your BRG claim is approved. While at first that sounds better, it (a) means you don't earn anything on a one-night stay, and (b) typically it's restricted to once a month or so, so it's not as useful for long stays or for multiple stays within a short time.

http://www.flyertalk.com/forum/choic...oom-again.html (Choice)

http://www.flyertalk.com/forum/inter...-feedback.html (IHG / Priority Club)

Still others, such as BRG, give you a slight discount or bonus points (most SPG points collectors take the bonus points):

http://www.flyertalk.com/forum/starw...er-thread.html (SPG)

The number of programs that officially let you earn points on third-party stays any more is tiny (if not zero). (To this first OP: You may have reading threads from years ago. Until several years ago, there were one or two programs that earned points on third-party stays, but one by one they went away.)

There may be some programs here or there that occasionally make mistakes, and let some stays booked through third-party sites earn points. But to me, that's not the same as it being official policy, because you can't be sure if your next stay will happen upon such a "nice mistake" or not.

A bit more common are programs which may not let you earn points, but do let you use elite benefits (if you have elite status there), on third-party stays.

(And then, as I mentioned in my other post right above, "third-party sites" are not the same thing as corporate travel sites. Quite different rules may apply to the latter.)