More fuel efficient...
To make an analogy, I'm going to rephrase your question so you understand what you're really asking.
"I'm having trouble getting my car to run on diesel, because it's cheaper than gasoline. Any suggestions?"
As people have mentioned, iOS devices (such as the iPad, iPod touch, and iPhone) don't run .exe files, which are DOS/Windows based coding. iOS doesn't even really run .dmg (which usually contain .pkg files, which contain, typically, compressed archives among other files, which contain .app files).
iOS and OSX both run .app files, however, iOS doesn't have the same structure as OSX. What this means is that iOS doesn't know what to do with those "other files" that aren't .app, that are typically used by OSX.
Windows uses .exe, which are setup entirely different and rely on registry entires and .dll (direct library links) rather than .pref (preference) files.
Before I spend too much more time letting you know all this technical errata, know that the iPad has a VPN for Cisco configurations built-in already. No need to install! You may need to confer with your system administrator for settings, but go to the General Settings>Network>VPN>Add VPN Configuration>IPSec tab (if you use Cisco). The settings documented in the link above will not apply to you unless you're trying to connect to THAT network.
As far as PDF reader, iBooks can read pdf files. To get it "synced", open iTunes from your syncing computer, simply add it as a file (File>Add to Library>filenamehere.pdf. If you don't like the simple iBooks reader, there are a number of pdf readers in the App Store. Unfortunately, you just can't get files from your intranet and install them, as it were, even if they were written for OSX.