I'm thankful you are concerned for your sick friends; often the most important thing you can do for them is to pray. The Bible says that "the prayer offered in faith will make the sick person well; the Lord will raise him up" (James 5:15).
However, I encourage you to tell them when you are praying for them (unless you sense it might be taken in the wrong way). In my experience, almost everyone who's facing a serious need (whether it is an illness or some other difficulty) will be encouraged by knowing someone is praying for them. Even if they've never given much thought to God, they know they may be in grave danger and will welcome the prayers of others. It may even cause them to begin thinking about their own spiritual needs and cause them to turn to Christ.
Let me urge you also to encourage others to pray. Perhaps you could help your church set up a way to notify people (perhaps by e-mail) who will pray whenever someone is sick or facing another need. Or perhaps you know of one or two people who are committed to prayer, and you could share requests with each other.
In addition, ask God to help you reach out to those who are sick in practical ways–preparing a meal for their family, baby-sitting, driving them to the doctor, and so forth. The Bible says, "Clothe yourselves with compassion" (Colossians 3:12).