Sell them both ways, apart and in a bundle. Keep the price of the bundle lower than the sum of all parts and somehow link to the parts from the bundle. This will show the user that hes getting a good deal.
I do not know any solid answers from research for this questions. Half the things you read say that '.99' makes some people interpret the price as being lower than it really is while the other half of research says that people interpret as being an underhanded tactic.
Personally, I prefer flat dollar prices. I'm much happier with $25.00/mo as opposed to $24.95 or $24.99/mo. I read them all as "$25" anyway and I prefer nice round numbers.
Like robflynn said, this depends on each person, it can be positive or negative.
In my case I would go with a flat price ($1 or $2) or perhaps a flat price with a little more like $1.20 or $2.40. This seems like it isn't a random price.