I prefer dosbox over native dos for most games given it's a bit of a pain doing all the old dox memory dances as well as joystick and sound card support. With the rigs these days most dosbox based games run just fine.
I still love F-15 Strike Eagle II (yes, I said II (two, 2, dos)) and F-117 Stealth Fighter from Microprose.
Age of Rifles still can't be beat.
I recently got Star Trek The Next Generation - A Final Unity installed under dosbox. Looks danged good for as old as it is.
I run Win98 under a VM just so I can play the Great Battles Series from iMagic. (The game's got a weird glitch under XP and higher where the right mouse click commands don't work..)
And then I found Good Old Games. OMG......www.gog.com