Ideally, you want to catch it before it hits the roof or in a different area. When I collected rain water I used a huge funnel - but there's a neat tool out there, the rain saucer..
http://rainsaucers.com/
If you have a tin roof then it's okay to collect the water after it runs off the roof. If your gutters are clean and not rusted or broken anywhere then again, it's okay to collect it from the gutter. I've used this method to water from my tin roof, into the gutters, and then into a 5 gallon bucket (I snipped the gutter so I could fit the bucket against the house and just slide the top piece inside the bottom piece when you're done)
If your roof is shingles or asphalt or something of the sort, no.. don't use the rainwater after it hits the roof
If the gutters are rusted or have anything in them that is contaminating them (if that makes sense) otherwise no, clean functioning gutters are fine for rain water collection.
The catch here is, is it contaminated when it hits the roof? What kind of roof is it? As stated above, if it's asphalt or shingles or something other than metal.. well, no guarantees! :thumbs: