Background
I wanted to run the 1995 LucasArts adventure game Full Throttle on my iPad 2 without jailbreaking it. SCUMMVM was, therefore, out of the question. I was one of the lucky few to snag a copy of iDOS (DOSBox for iPhone/iPad) before Apple plucked it from their App Store last October, however. I got it working well but I hit some snags along the way. Here is how I resolved each.

Copying game files from CD into iDOS
I zipped the contents of the CD, then dragged the zip file into iDOS via the clunky iTunes file sharing thing under iTunes > iPad > Apps. I was sure to make the filename all lower case, as there's a bug in the unzip program that's included with iDOS that prevents unzipping of files with capital letters in the filename. Once the zip file was on the iPad, I opened iDOS and simply typed UNZIP FT.ZIP and waited a few minutes. I deleted the zip file at that point.

Getting around the need for the CD without a crack
After installing the game inside iDOS (no snags there) I tried running it via THROTTLE.EXE and was prompted to insert the CD. I was able to run it without the CD if I ran FT.EXE from the RESOURCE directory from the CD but that executable doesn't allow the player to save his game, so that was not an option. I could have copied a disk image to the iPad and mounted it as D: but I wasn't able to make a compatible disk image from my original CD. My workaround was to mount the C: drive as D: so that both C: and D: contained the exact same data, including the contents of the Full Throttle CD. Apparently the game just looks for a drive D with the right files on it. Once I did that, I could run THROTTLE.EXE and it didn't ask for the CD. To actually mount C: as D:, I did this:
Go to Z:
Type MOUNT and I saw the (long!) path that the C: drive was mounted automatically using. I noted that path.
Type MOUNT D <long path from above>
That's all. That essentially mounts the same folder that C: uses but for D: as well.

Correcting mouse movement
The game opens and sound works (the installer's sound setup utility's "Express" setup detected a Sound Blaster 16) but the mouse movement is wrong. It moves horizontally at the right speed but vertically it only moves at about 1/2 speed, which makes the game very hard to play. This was hard to fix but I finally found a way. I used a program called MOUSEOFF.COM that I found on another VOGONS forum thread (citation needed). Running that disables the built-in iDOS mouse driver altogether. I copied an ancient MOUSE.COM from an old boot disk I had lying around onto the iPad as well. I grabbed EDIT.COM while I was at it, which was useful later. I ran MOUSE.COM with movement adjustment switches to get the effect I needed:
MOUSE.COM /H55 /V100 /P4
That means horizontal movement is 55% of its normal speed, vertical is 100% and the acceleration profile used is 4 (unaccelerated -- I don't like mouse acceleration on low resolution games). Note that only values up to 100 are accepted, so I couldn't have made the vertical axis 220%, as I'd originally intended.

Fixing choppy sound
The game's performance is barely playable. It feels as though I'm running it on a computer that's just too slow. The only thing I know to do for this is to press Ctrl-F12 to increase the CPU emulation to 105%. That's as high as it can go. That extra 5% made a big difference though, and sound is much smoother, although animations are poor during some cutscenes. If anyone has any tips for speeding this up a little more, I'm interested to know.

Making all of this much simpler
I created a batch file called C:\FULL.BAT that contains all of the commands listed above. All I have to do now is launch iDOS, type FULL and hit Enter. Once the game starts, I press Ctrl-F12 and I'm golden. The full contents of my batch file are below. Let me know what you think! (And please don't tell me to jailbreak and save myself a lot of work; I'm well aware of that option but chose to try it this way on purpose.)

FULL.BAT contents
@ECHO OFF
ECHO Preparing Full Throttle
ECHO.
ECHO.
Z:\MOUNT D /var/mobile/Applications/9DA6A9D1-A6C8-44D8-A763-661061258D77/Documents/
ECHO.
C:\MOUSEOFF.COM
ECHO.
C:\MOUSE.COM /H55 /V100 /P4
ECHO.
C:\THROTTLE\THROTTLE.EXE