Depends on the GPUs you are using, if you are running 2 in CF or SLI at 8x/8x you wont take much of a performance hit versus running 2 at 16x/16x, its a 5% hit at most so 8x doesnt matter too much since only high end cards suffer any notable performance hit.
If we are talking about something like 2 GTX 460s vs 1 GTX 480 then the 2 GTX 460s will give better performance, if we are talking 2 5770s vs 1 5870 then the single 5870 will give better performance so it really depends which cards you are talking about.
I you are looking to see if going from 1 card at x16 vs two of those cards at 8x/8x, the fact that you have half the bandwidth won't effect you by more than 2%-4% less performance compared to x16/x16. You will still be significantly better off than one card. That said, keep it mind that this is the assumption of using the same card for sli/crossfire or the same card alone.
If you are thinking of using one card alone, or two lesser card together, you should probably tell us what those are so we could give you an idea of what the performance would be.
I have always been a fan of single GPU.
Not all applications benefit from dual GPU and single GPU also runs quieter, lower power consumption, more efficient (you're not going to get x2 the performance just because you have x2 graphics cards), and in many cases physically fits better (not cramped; allowing more air flow) in the case.
The only reason why I would consider dual GPU is if you already have one and would rather xfire/SLI than throw away your old one; but even in this case you will most likely have to replace your PSU which can be rather expensive in itself.
As for the x8 x8 vs x16 x16 issue, this isn't really an issue for the graphics cards available now, so don't worry too much about that. But to answer your question bluntly and directly: the x16 x16 will give better results
but but but, not necessarily true that when you pop in a 2nd card your PCI's will become x8 x8. In many boards (like lga1336 for intel i7's) you can have dual gpu running at full x16 x16.
I'm also a fan of single card solutions. I understand that adding a 2nd card down the road can be a simple and cheap way to increase performance by a fair margin, but if you consider the fact that you probably had to pay more for a board that support multi-card setup and probably had to get a PSU with more headroom, I don't know if it ends up being that much of a cash saver. You also have to consider that you can sell your old card.
However, if your MB and PSU already supports multi-card, then getting a 2nd card is certainly the best way to go.
Here is a post I put in a forum recently about a guy asking if he should get a new card or another 4870, and here is some relevant info i posted:
"it looks like, surprisingly, 4870s are reaching in the mid to high $90's (USD) range on ebay. (compared to the GTX+ 9800-which came out in the same month, for $100 more, no less-and seems to be had on ebay for under $100 easily.) If you can rely on a brand new video card keeping the same value as the 4870 (and the 4xxx series in general) in 2 years, then selling a card and putting that to a new card is at best a little better than getting getting one GPU and a 2nd later.
In most cases, when a card's value isn't held onto nearly as well, you probably are better off planning for sli/crossfire (assuming you bought a psu that can handle it when the time comes), but in your case, I think you will very much benefit trying to sell you 4870 and buying a new card (somewhere in the $200-$300 range)...I think you could get a 460 or 5830, and if you really look for sales and are open to the the upper range of your budget, you can get a 5850 or 470 for around $250-$270."
if you are getting a gaming pc, there is a very likely chance that nowadays it already has some sort of crossfirex or sli capabilities. I would say that if you are spending at least $100 on the mobo, you won't have top pay extra for multi GPU support.
Getting a PSU isn't prohibitively more either, but I would say $30 more is reasonable for a standard PSU, like a Corsair HX or TX. So the point remains that unless your GPU is selling really high two years down the line, it would most likely be feasible to set up a 2 GPU configuration.