OK, here is my advise. First, file the 2008 return. How you do it, is up to you. You could use a tax preparer (agent), or software, or online resources -- whatever works for you. Then, after you are up to date, you need to get copies of your Tax Account Transcripts for the years 2007 through 2010 (i.e., one year prior to the year you failed to file through the most current transcript available). While you are at it, order the Tax Return Transcripts (which are more detailed than Account Transcripts) as well, for each of these years. The IRS will provide these to you for free. You can order them online or through a toll-free number.
When you apply for Naturalization, in the Form N-400, mention that you (1) failed to file the return for 2007, (2) did not owe the IRS any money at any time (you were due a refund), and (3) have enclosed copies of Tax Account Transcripts (for years 2007 through 2010) with the Form N-400.
Admittedly, this is a bit of work. But, you may get money back from the IRS (after the penalty is deducted for late filing).
Now, here is my story. My wife and I have had our green cards since 1992, and did not really feel the need to naturalize. In 2008, my wife received a job offer from a government agency, and the need to naturalize became urgent.
Unfortunately, during the years 2003 through 2007, I had filed for extensions on my tax returns, for each of those years, but never filed a final return. [During those years, my life was affected by much turbulence and crisis, and not filing my tax returns was only one of the many lapses I was responsible for.] Anyhow, in 2008, I went to my local H&R Block, and had them file the back tax returns for 2003 through 2006. For the year 2007, I managed to file the return by myself. The good news was that IRS actually refunded me money for the three prior years (after deduction of penalty); they do not issue refunds for returns that are more than three years in the past.
Then, after this process was over, in 2008, my wife filed her N-400, using the steps I have outlined above. We (meaning with my help, she) included a statement of explanation and the tax account transcripts for the years 2003 through 2008. Her naturalization proceeded pretty smoothly, and was completed in about three months and a half. In February of this year, I submitted my N-400. See my signature for my time line.
Hope this helps.
Also, please be aware that my advice should not be construed as professional legal or tax advice; I am merely sharing my experiences with you as a layperson.