Apple's iPod firmware (since 3.0) is designed to run each app in its own memory process and to not let that app's background services write to or interfere with any other part of the system or its memory without being an app issued by Apple that came with your iPod.
The only way(s) you could have intercepted an ipax virus (ipa is the file extension for apps on an iPod touch, e.g. Falldown.ipa - ipax is the extension for an app which runs in the background service, e.g. Falldown_Submit_Score.ipax), which DO exist, would be:
* To have downloaded a disguised ipax file and mistaken it for an MP3 or image file, then synced it to your iPod's music or pics app (these apps would also mistake it as an image/MP3 and, being apps created by Apple, would allow these ipax files to access your firmware's system root process, infecting the iPod).
* To have allowed a malicious app to send push notifications or use the location service (this could freeze the iPod by spamming its processor with millions of requests in the background).
* To have jailbroken your iPod (This is the most likely reason, for it disables all of the protection mentioned in my first paragraph. This does, however, allow for more convenient features, e.g. running third-party apps in the background). Side effects of this include memory leaks from the instability of third-party services requesting the same resources at once, causing freezes and SpringBoard (the GUI) to crash. MobileSubstrate is a jailbreak service that enables a safe mode when the latter event occurs.
To fix your iPod, I would suggest:
1. Open iTunes
2. Plug in your iPod
3. On the left sidebar of iTunes, find your device
4. Click its icon
5. Click Restore on the Summary tab of the iPod screen
6. Follow the instructions given in the restoration
7. Uninstall any apps you installed that may have caused the crashes or virus-like systems. Do this on iTunes.
As for finding an app or program to scan your iPod, I've never heard of one. Good luck, though!