Hi, Here's my 2 cents...

1) what's the best way to incorporate the check out system/payments? I know yahoo and amazon does but they charge a FEE per transaction and i think it's a rip off.
I think if you are still interested in selling on eBay, it's important to find a solution that keeps your data in one place. Check out the Auction Software Review page about these programs. Most of these (including Laris, the platform offered by the e-commerce experts at Sell Center) have payment gateways built in. The best part is that you only have 1 inventory system for multiple sales venues.

2) who has the most simple inventory program?
I agree that this is totally subjective. It's all about testing various programs, getting free trials and seeing what you like the best.

3) who do you guys recommend me to host my website with the ecommerce program?
If you're just starting out and have a lower budget, go with a shared hosting solution. I've tried a ton of them and the best shared host that I've found is BlueHost.com.

If you are ready to move up, get a dedicated server. From experience, Aplus.net is amazing. Their customer service reps are geniuses - the last time they called, they showed us how to do a bunch of Mod Rewrites... very cool.

I hope this helps!