I have a Jamis Bosanova and use it for almost everything. I tour on it, I commute, ride in town, group ride, country ride, etc. I am currently running the stock Alex wheelset with formula hubs. This bike has bb5 disc brake BTW. I am using 32c Vittoria Randonneur Cross tires for touring and dirt road riding, which they are great for. They are a bit on the heavy side for city and faster riding. I am wanting to get a second wheelset and put a set of 28c slick tires for those rides. I am now wondering about the cassette, I have a tiagra rear derailleur and a 9 speed sram 12-26 currently. I would not mind putting a 12-32 MTB cassette on my fat tire wheelset for touring and rough road riding. That would mean I need a MTB rear derailleur. On the skinny tire wheelset I would like to keep the gearing higher with a 12-26 or something close.
Would a MTB rear derailleur work correctly when changing wheels with such drastically different cassettes? What about other solutions to make this wheelset viable?

not that it matters for the rear, but I am using a VO 48 36 28 triple crankset.

Sort of in the same boat here. Currently on a cyclocross bike running Alex R500 w/ 32 Randonneur Cross tires. Looking for a set of lighter road wheels and tires.

Did you find any good deals?

you using disc brakes? if so the https://www.nashbar.com/webapp/wcs/st...0052_520037_-1 and corresponding front are what I am thinking about ordering with some continental GP4 season in a 28c. the cassette is what I am not sure about

Many of my bikes have multiple wheelsets but I haven't done this with disc brakes yet. I know the disc has to be in exactly the right position or it'll rub the pads so watch out for that.

As far as gearing, the MTB derailer will handle both the 12-26 and 12-32 cassettes fine. Just make sure to size the chain for the larger 12-32 cassette. You will probably have to add links to your current chain, or better yet just get a new one. If the cassettes are not in exactly the same place between wheelsets you will have to do a little fiddling with cable tension and possibly limit screws when you swap. But if you have cup-and-cone hubs you can play around with the spacers to make the swap seamless. Don't know what that'll do to your rotor situation though.

If I get the issue correctly, there's never a problem using a derailleur for less than it's rated capacity. That means you can use the mtn derailleur for both the wider and narrower cassette. The chain length will likewise be set according to the wider cassette, and be fine for the smaller one since the starting sprockets are the same or close to that.

You should expect to have to make minor rear derailleur adjustments when swapping wheels; given manufacturing tolerances even identical wheels and cassettes will differ slightly. You will probably need to change the B-screw adjustment to compensate for the differences in large cog size, for optimum shifting performance.

Expect minor changes in your brake adjustments as well.