There are quite a few options:
Leave natural colour & then wax
Leave natural colour & then varnish
Stain & then wax
Stain & then varnish
Paint & then wax
Paint & then varnish
Use a thick floor paint that doesn't need any further protection.
Basically you need to decide what colour you want and what type of finish you want and this is quite a personal choice. As above either stain or paint will generally need some sort of protective coating applied. Some products do both in one, others you will need separate products.
You need to consider where the floor is and how much wear it will get - e.g. a hallway will need much more protection than a rarely used spare bedroom. What is likely to get spilt on it? Do you want a shiny finish (go for varnish) or a matt finish (go for wax)?
Also consider the style/period of your house and whether you want something to suit the period or something more personal to you.
My personal preference is natural colour waxed if the floorboards are hardwood (oak or something) or a slight stain and then wax if they are pine. I absolutely hate pine floorboards covered in a yellowy varnish - but judging by lots of the houses I've seen others love that look.... I have pine floorboards which I sanded down (they had been painted bright purple ) and then applied 3 coats of this in natural oak. The finish is great, you can spill pretty much anything on it and it doesn't soak in just wipes off.
In terms of cost, depends if you are having someone do it for you or doing it yourself! The products themselves are relatively simiar in cost but it can be quite labour intensive(e.g. 2? coats of paint/stain & several coats of wax/varnish with rubbing off inbetween). Of course companies who do it probably have special machines whereas I was down on my hands and knees with a brush!
Not sure if that is much help but imo it really is a style thing rather than anything else.