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Question

Why does Nehemiah ask God to remember his good deeds? I noticed that Nehemiah frequently asked the Lord to remember his good deeds. When I read that, I can't help but consider what the prophet Isaiah says about our good deeds being as filthy rags before the Lord. Personally, knowing the depth of my own sin, I could never bring myself to ask the Lord to remember the good I have done for Him...it's seems, well, presumptuous?!

Answer

I think that it is more accurate to see that Nehemiah is asking in general for "God's favor and blessing upon his life." So, the book ends (13:31) with these words: "Remember me, O my God, for good." Another translation is "Remember me with favor, O my God." He is asking for God's blessing and favor.

He is not asking so much for God to remember him  on the basis of his good deeds, but to work so as to preserve them.  This seems to be the case in 13:14.  Ultimately, Ezra and Nehemiah did not see the success that they would have hoped for.  Ezra and Nehemiah were faithful, but the people did not follow through to keep the vows that they made (recorded in particular in chapter 10).  So, part of Nehemiah's request is for God to make his works mean something; he doesn't want them to all be for nothing! 

Next, there is the idea of Nehemiah hoping (and asking for) God will be pleased with his works.  This, I think is the heart of your question.  This sense comes out the clearest in 5:19.  This concludes a short prayer (5:14-19).  Nehemiah has done these works out of "the fear of God" and unto the Lord in worship.  This carries with it the obvious idea of reward.  Faith is confidence that God will reward those who truly seek him (Hebrews 11:6).  I think the following words from Matthew Henry sum it up well and will help you grasp some good application for yourself:

Those who truly fear God, will not dare to do any thing cruel or unjust. Let all who are in public places remember that they are so placed to do good, not to enrich themselves. Nehemiah mentions it to God in prayer, not as if he had merited any favour from God, but to show that he depended upon God only, to make up to him what he had lost and laid out for his honour. Nehemiah evidently spake and acted as one that knew himself to be a sinner. He did not mean to claim a reward as of debt, but in the manner that the Lord rewards a cup of cold water given to a disciple for his sake. The fear and love of God in the heart, and true love of the brethren, will lead to every good work. These are proper evidences of justifying faith; and our reconciled God will look upon persons of this character for good, according to all they have done for his people.

There are great applications to be made in our lives based on these passages.  Nehemah was a man of prayer.  I have been asking more and more in the last year for God to bless my family and Riverside.  Somehow, I got it in my head at one time that this was inappropriate.  The release has been wonderful: Our hope is in God!  Along those lines (a second application), let us labor to do good works that will please God and result in eternal reward.  Our sacrifices are not in place of the cross.  They are because of the cross and as a result, we hardly feel that we can even call them sacrifices.  Isn't God awesome!