No question - Clean the deck. Otherwise, what dust and dirt there is that's been accumulating on the deck for 'a few years' will be what absorbes the stain; NOT the wood. There are 'washing solutions' you can use to clean it and there is the old Power Washing method.
I would go with as transparent a stain as you can. Some folks will argue (and argue they will) that a dark stain is fine. But from experience, if you don't like the dark stain, it's nearly impossible to remove! 2 years ago, we stained our pressure-treated deck with, well you guessed it, a dark stain. (Not to dig on my wife because she likes it but I DIDN'T pick it and I don't like it.) You can see the 'wear areas' where people walk and such, you can see that it doesn't cover uniformly, and I can't think what else there is I don't like about dark stain (at the moment.) AT least with the clear stain, because it's clear, it's more forgiving.
I suggest you visit your local Paint Retailer (found in the YELLOW PAGES under PAINT - RETAIL) for a high quality sealer. I'd stay away from the Home Depots and Lowes types-of-stores. You'll get a good deal on stains and sealers and paints but you get what you pay for. For the extra $$$ you spend 'elsewhere', you'll be pleased. Penofin, Olympic, CWF, Woleman's, SHerwin-Williams ,to name a few are worth their money. See Consumer Reports (1999) for some related info. (Apparently, they're doing more testing.)
Be SURE that the stain/sealer you use is appropriate for the type of deck you have. (You didn't say ...) My best to ya and hope this helps.
PS: After this afternoon, I won't be back until Monday morning but others will be around ...