Most people just replace what they had with the same thing. Wood is generally the choice for living areas, while tile is the choice for wet areas such as kitchens and baths. You could also go with tile and stone in high traffic areas. As you should know, brands can be meaningless, Pergo is one of the most well know floor covering, but ask anyone who knows flooring and they say that it's okay if you don't mind replacing it in high traffic areas on occasion. The truth is everything falls apart eventually, so get what appeals to you.
When it's wood, I like solid, it is two to three times more expensive tha laminates, but it can be refinished. Engineered is actually better than solid in certain respects, but costs more and can only be refinished once or twice.
As for tile, know that glazes make it slippery in wet areas and if it chips the clay body will show through. I like porceleins for that reason, I think that they're a bit harder, but they are also the same color all the way through.
I'm not a fan of natural stone because it needs to be sealed annually, but the colors are much more dramatic than what you can get from wood.\
As to where to go, Lumber Liquidators are all over the place and they actually have good prices on quality flooring, better than what the big boxes have. I haven't bought from LL, and I am always wary of a good deal, but if the price can't be beat and you're having a professional install it, that would save money.
It's actually not too hard to install flooring yourself and you can save a bit of money by renting the necessary equipment, it just takes time and you need to be precise. If you don't have patience, stay far away, it will only give you heartache and a bad floor.