I'll take considerable heat for my opinion on this, since the IRS encourages electronic filing, as do many accountants. In fact, the IRS boasts that two out of three 2008 returns were filed electronically. Clearly, electronic filing is the thing of the future and will be required for every return someday soon.
Until then, I suggest filing the old fashioned way, particularly if you're worried about an audit. Why? Paper filing means it's more work for the IRS to access all the information in your return. Your duty as a taxpayer is to be truthful and accurate, but you don't have to make it easy for the IRS.
If only the government were required to be truthful and accurate.