The long of the short:
Oil based products by in large are more durable and provide better adhesion and stability over time.
The reason that so many new products are water based is simple... It is NOT new technology in water based coatings, but rather the fact that they very compounds (VOCs) that make coatings durable have been banned and/or regulated to the point of extinction or extreme supply costs.
You will find that most manufacturers tout their water based products as "new technology", "environmentaly friendly", "easy cleanup", etc.
The reality is that they are nowhere near the quality of their older coatings that can no longer be made. This is not just a consumer problem, it is industrial also. Coatings have not improved over the last decade or so, they have taken a huge step backwards.
We now paint bridges every 5 years instead of every 20 years.
Don't get me wrong, there is a place for both oil (alkyd) and latex (water) based paint products and oil and water based urethane products.
With regard to THIS subject...
Oil based wood finishes will give a warm feel and will amber over time. This is desirable to MOST people. The oils penetrate the wood surface and form a deep protective coating that is very desirable in damp conditions.
Water based finsihes will have a bluish cast to them and tend to wear much differently. The solids content does not penetrate as deeply and therefore the wood is not as protected in harsh environments.
There are MANY other facets to the conversation, but you will find that MOST informed woodworkers prefer the oil based products for MOST projects. As I mentioned, water does have it's place.
As for brands of finish.. I am not a minwax fan at all. I use the stuff for some projects (like our hardwood floors) but use the General finishes products for everything else.
As for the environment... not everyting that appears to be a good idea really is. The VOC ban and regulations have cuased the coating re-application rates to skyrocket as well as the amount of goods that get scraped due to coating failure. Look at CFL lightbulbs and the enviro morons that want to make incadescent bulbs illegal in favor of CFLs. Somebody forgot to remind them about the fact the the CFLs manufacturing process negates any savings it would ever have on energy consumption, let alone the fact that the thing is made of PLASTIC and MERCURY, COPPER, LEAD etc...
Enjoy...
Grab a pint of each and slap em on some of the wood you plan to use 
