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This is a very good question because the most important thing you can do for an unsaved spouse is to pray earnestly for them.  Remember that "the effectual fervent prayer of a righteous man (or woman) availeth much"  (James 5:16). "I exhort therefore, that, first of all, supplications, prayers, intercessions, and giving of thanks, be made for all men."  (1 Timothy 2:1)

One thing I have just learned and started to apply to my prayer life is to claim God's promises for others.  The Lord tells us in Isaiah 55:11  "So shall my word be that goeth out of my mouth: it shall not return unto me void, but it shall accomplish that which I please, and it shall prosper in the thing whereto I sent it."  The Bible is filled with promises and they are there for a reason.  God's word is powerful (Hebrews 4:12).  Jesus tells us to "Ask and it shall be given you" (Matthew 7:7) and "If ye shall ask any thing in my name, I will do it." (John 14:14).  Next, you need to believe: "Therefore I say unto, whatever things you ask when you pray, believe that you receive them, and you will have them." (Mark 11:24).   Then you should claim God's promises for the people you are praying for.  Always give thanks to God for hearing and answering your prayers: "O give thanks unto the Lord, for he is good: for his mercy endureth for ever."  (Psalm 107:1)  "Oh that men would praise the Lord for his goodness, and for his wonderful works to the children of men!"  (Psalm 107:8).   No matter how the Lord chooses to answer our prayers, we can trust that His ways our higher than ours (Isaiah 55:8-9) and that He always knows what is best.  We need to be thankful regardless of whether or not we see immediate answers to our petitions: "In every thing give thanks: for this is the will of God in Christ Jesus concerning you." (1 Thessalonians 5:18)

Here are some promises that you can claim as you pray for your spouse: "The Lord is not slack concerning His promise, as some count slackness, but is longsuffering toward us, not willing that any should perish but that all should come to repentance." (2 Peter 3:9).  God doesn't want your un-saved loved one to miss out on eternal life, so pray that the Lord will bring them to repentance so that they will choose to turn away from their sins and accept Jesus into their heart.

"And I will give them a heart to know me, that I am the Lord: they shall be my people, and I will be their God: for they shall return unto me with their whole heart." (Jeremiah 24:7). "A new heart also will I give you, and a new spirit will I put within you: I will take away the stony heart out of your flesh, and I will give an heart of flesh." (Ezekiel 36:26) Pray that God will change the heart of your spouse so that they will have a desire to walk with the Lord.

"Therefore said He unto them, The harvest truly is great, but the labourers are few: pray ye therefore the Lord of the harvest, that he would send forth labourers into his harvest." (Luke 10:2). Ask God to send someone into their life who will lead them to Christ and will serve as a positive influence.

Don't forget to pray for yourself as well, that the Lord will help you to be a uplifting example for your spouse.  Ask God to give you "the mind of Christ" (1 Corinthians 2:16 & Philippians 2:5) so that your actions will represent the Savior and your influence will be a holy one.  Remember that Peter instructed Christian wives to witness to their unbelieving husbands through their righteous lifestyle and behavior (1 Peter 3:1-4). This counsel can also be applied to the Christian husband in relation to his unsaved wife.

The main thing to remember is this: Don't ever be discouraged!  God often uses difficult and trying circumstances in order to refine our characters and prepare us for His heavenly kingdom (Romans 5:3-5, James 1:2-4). Don't ever stop praying "but in everything by prayer and supplication with thanksgiving let your requests be made known unto God. And the peace of God, which passeth all understanding, will keep your hearts and minds through Christ Jesus." (Philippians 4:6-7)