I installed WSS 3.0 as part of Search Server Express 2008 installation package, and used SQL Server 2005 Standard as backend database, all of them in one server. What's the best backup strategy for me? I've already upload a lot of document in the site Document Library. Is it enough to just backup the database? Can I use stsadm backup on a large data (almost 100 gigs)?
Have you already looked at this question? It may give you the answers you need.
Yes stsadm is fine, it will backup the database contents and site. You should also do a SQL backup of the backend db just in case. We have a scheduled task that runs stsadm daily and dumps the backup to a folder. From there our backup software slurps it up and puts it on tape.
EDIT - it appears my advice above is only good for small (<15GB) sites according to Technet. For bigger sites they recommend not using stsadm. This is news to me too, so I'd better read the link!
If you're dealing with a single server and not too much custom code, SQL backups should be adequate - for out of the box stuff you can install sharepoint and reattach a content database to get all your documents back.
Backing up of global configuration (such as search properties) and any custom features installed is a bit more complicated - simple SQL backup may be good enough, but it may fall over if things like server name are different on the new server.
Having spent the last few days trying to upgrade a 50GB content database, I'd definitely recommend you split the database into smaller pieces before you have to do it at short notice.