To do this, you need to access the MobileScrobbler executable inside the application bundle on your iPhone and issue a command along the following lines:
./MobileScrobbler -track "Shimmer" -artist "Fuel" -album ""
The developers write, saying the album string will be optional--you can pass an empty string as shown here.
This is a great little feature that shouldn't be overlooked by anyone who has command-line access on their iPhone or iPod touch. For a further preview of Mobile Scrobbler 1.4, check out this screenshot tour.