I've posted about the recent SalesForce.com outage in my notebook. It is something for non-profits to consider when deciding on software to manage their donors and fundraising. Where is your data? I am not trying to scare anyone, but it is something you will eventually have to deal with if you use an online service for your fundraising database. Assuming they have the features you need, these services can do the job, but your data (your organization's lifeblood) is being managed by someone else. Your ability to access it depends on their ability to keep it available. Make the necessary preparations -- make regular, local copies of your data and make sure you can get to those records in the case you can't get online.
The fact that GiftWorks is not a web service doesn't mean you are in the clear from the problems. In this case, you manage your data. You still need to do regular backups to another computer or media. Hopefully we make this an easy enough task that it shouldn't be a problem for you.
One thing that GiftWorks does have over web services is that you can access your data anytime you want to -- you do not need to be online. You can also copy the datase to a laptop and take it with you for the weekend.