I know minwax makes a water based stain that is supposedly low fumes, but I've never used it. The range of colors aren't all encompassing and you can't use every type of clear coat over it.
I have used minwax oil based stains and have been happy with the quality. The odor usually dissipates quickly if you have decent ventilation (you should have good ventilation anytime you are finishing stuff). The top coat depends on your application. I have used multiple coats of minwax wipe on poly (satin finish) and have fallen in love with this product (after years of using brush on). It has worked on my restored doors and moldings. It is impossible to get runs and drips and the finish looks like a hand rubbed low gloss application. Drawbacks include that it is not to be used on floors or other rugged use areas and it isn't the cheapest stuff on the planet - but then a little goes a long way with this. For an exterior door I have, I used a spar uerathane that has stood up very well to temperature extremes.
There are water based poly's that have less noxious vapors, but I find the wipe on poly to be not all that bad and certainly less noxious than brush on.
No affiliation with minwax, just like their products for the price.
BTW, if anyone is interested in an all encompassing survey of paint strippers, I've tried them all over the past 2 years:-)