With direct sales you have the 100% of royalties...
Don't forget expenses for servers and bandwidth. Many portals/distributors I've seen host the game for you, so you save that money. I've seen a post on Aquaria somewhere stating how much bandwith they needed in the beginning and it was MUCH

.
The best online payment service i used was the one Bit Blot chosed for Aquaria:
Maybe it's just my experience but Plimus is a bad choice. They are the reason why I haven't bought Aquaria and Noitu Love 2. There is almost always some issue. Either they block your email adress because it is a "free" provider (blocking a major national email provider is a really smart move :D) or they send you to non-existing (404) Paypal-pages or if you finally manage to buy something they harass you to give them your phone number. Trying to get support on these issues is also a nightmare or just plain impossible. They don't seem to be very competent in my experience.
Fortunately there are several other companies offering the same or better services. Depending on whether they charge for setting up a store, I'd say choose at least two different ones, so your customers can choose.
Many distributors/affiliates don't restrict your ability to sell your game via multiple channels. So you might as well offer it to as many portals/distributors as you like and also sell it on your homepage. Depending on your game and the portal/distributor, you can reach different audiences you would not be able to reach on your own. I'd expect your "name" to be less noticed if you sell via portals though, because their name and their brand is prominently placed everywhere on the site.