In a nutshell, the eBay apps you've mentioned are all listing tools, all of which helps eBay sellers list, manage, and optimize their product listings. Using either of these apps on eBay does not damage your account for as long as you are using it within eBay's terms and conditions.
The main difference I guess is with Auctiva, the paid subscription has an interactive dashboard that allows one to gain insights into sales data, profits, and other metrics. 3Dsellers has a Helpdesk that provides an automatic customer support to buyers. And finally, Channel Advisor offers preloaded templates for eBay catalogs.
I'm only highlighting the main difference here but it's up to you to decide which app works best for you. They should have like a free trial on their site to help you decide better.