I am sorry to resurrect such an old thread, but I have found a solution. I can get butter smooth perfect scrolling with no stutters.
I am one of those who can't play a game if the scrolling isn't smooth. So I was also looking for a perfect solution.
Here's what I did in the end, what is working for me and I hope will help some of you.
I ended up using DOSBox SVN-Daum, UPDATED Jan 27, 2014.
The first trick was to use "output=direct3d" under [sdl] and "vsyncmode=host" under [vsync].
The second trick was to find out at what fps game is being rendered in the egine. Some are rendered at 30 fps, others at 35 fps, then 60 fps and 70 fps. These are the most common ones. Some are rendered at 1/2 fps of the refresh rate, but you still need to find out if 60 Hz is correct or 70 Hz. Here you just do trial and error. Set 60 Hz refresh rate and run the game to see if it's running as it should. If not, switch to 70 Hz and try again.
The third trick was how to keep monitor refresh rate at certain value when switching DOSBox to fullscreen. I came up with two options. First is to set "fullresolution=" under [sdl] to your monitor's native resolution, so when you switch DOSBox to fullscreen it doesn't get changed. But this way the aspect ratio isn't perfect. At least not for me. You can set "aspect=true" under [render], but I personally like the second option better. And the second option is to set "fullresolution=1280x800" under [sdl] and set your graphics card to do GPU scaling. I will not go into details for this, because it's different for nvidia, amd, intel, etc. so find instructions for your graphics card on google. I have nvidia, so if there will be enought interest, I can do a follow up post to explain more into details.
The reason for GPU scaling is that you don't want the resolution to change once you set it at XxY@60/70Hz, where XxY is whatever resolution your monitor will run @60/70 Hz. I expect all monitors run @60 Hz with native resolution, @70 Hz could require you to use a lower resolution, though.
Without GPU scaling the resolution will change when going fullscreen and will probably switch from @70 Hz to @60 Hz, but if you need @70 Hz, then this is not what you want.
Oh, there's one more trick... How to get your monitor to run at 70 Hz... For me, I had to add manual resolution in nvidia's control panel and "Enable resolutions not exposed by the display". CAUTION! If you're going to try this, there's a small chace you can damage your monitor. So bare that in mind. I take no responsibility for any damage. If you are going to try it anyway (I did), start with lower resolutions first. For example 800x600@70Hz.
Here is the list of games and their fps and refresh rate at which you need to run them for smooth scrolling:
Games that need to be run @70 Hz:
In search of Dr. Riptide - 35 fps (you can also run it @60 Hz with 30 fps, but then it's clearly its not native speed)
Tyrian - 35 fps (you can run it @60 Hz with 30 fps, but it's slowed down compared to real DOS).
Doofus - 70 fps (you can change the refresh rate in-game between 70 Hz and 55 Hz... my monitor supports also 55 Hz, so I can run it at both speeds)
Doom - 35 fps (runs at this fps no matter the refresh rate, but it's smooth only @70 Hz, or a refresh rate that's multiple of 35)
Commander Keen in Goodbye, Galaxy - 35 fps (smooth scrolling is the most obvious when you start the game and the id logo scrolls up and then the words COMMANDER KEEN are scrolled horizontally)
Games that need to be run @60 Hz:
Epic Pinball - 60 fps
Jazz Jackrabbit - 60 fps
Micro Machines 2 - 60 fps
Superfrog - 60 fps
So, to sum it up, you need to:
1) Use the correct refresh rate based on fps of the game you want to play with smooth scrolling.
2) Use vsync.
The described solution is finally giving me the same results as if I run the games natively on an old Pentium PC with MS-DOS 6.22.
Before I came up with the described solution, I was using DOSBox ECE for a long time. With output=opengl and forced vsync in my graphics card's control panel. It kind of worked. Of course I also had to switch between 60 Hz and 70 Hz refresh rate. But there were clear problems... Jazz Jackrabbit worked flawlessly only in-game. Menus were stuttery, slowed down, when you exited the game, the end animation (the circle) would be veeery slow, etc. None of these problems are there with the solution described above.
As a bonus, here's how you get Jazz Jackrabbit 2 to run smoothly:
I am so glad I finally did it. I wish to all who love and need perfectly smooth scrolling that you succeed setting it up. Please contact me if there are things that are not clear enough or for suggestions with your specific hardware. I will try and help you to get the smooth scrolling, because I know how much it means to us who just need it. 😉
EDIT: Typos + added games to the lists.