Knapdog stick with 25s. I have tried 28s and 23s on my tourer, too heavy and too unforgiving respectively, and now decided 25s are the best combination for touring. Although when I checked pressures a few weeks ago I was shocked to see I had fitted a 23C on the back. No wonder the ride is a tad harsh. I must have fitted it as I didn't have another 25C kicking around when the last one wore out and forgotten about it. Fine on smooth roads though. I have 23C on the front irrespective of the back. The 28s will have a larger rolling circumference and will give marginally increased comfort due to the increased thickness of side walls compared to 25C. They will also make your bike feel slightly less manouevrable and are of course slightly heavier depending on tyre you choose. My tyres have all been Specialised Armadillo All Condition Pro tyres 23, 25 and 28C. Will shortly be trying Vittoria Rubino Pros as I have these in 23C on my road bike and like them a lot.
Of course tyre pressure will greatly affect ride quality and comfort. Why not just reduce the tyre pressure by 10-15 psi? I wouldn't go below 100psi though as this makes the tyre too soft and means lots of wasted energy.
If you are touring with a heavy load and few spokes in your wheel on factory built wheels I would say go for 28C tyres as they will be more forgiving on your wheel. If you've a 32H or better a 36H hand built strong wheel then 25C will be fine on a touring wheel carrying weight as will 23C for smooth roads.
If riding rough surfaces I would use a minimum of 28C.
Oh and +1 Alun's post re clearance issues with mudguards as already stated 28C have a significantly larger rolling cicumference. You will also have to re-calibrate your cycling computer if you have one.
Hope this has been of help.