If you are using a database that supports map-reduce, like couchdb, storing tags in a plain text field or list field is indeed the best way. Example:
tagcloud: {
map: function(doc){
for(tag in doc.tags){
emit(doc.tags[tag],1)
}
}
reduce: function(keys,values){
return values.length
}
}
Running this with group=true will group the results by tag name, and even return a count of the number of times that tag was encountered. It's very similar to counting the occurrences of a word in text.