Installing software from package sources Vs downloadable .deb files
Apart from getting automatic updates through apt-get upgrade and chain updates from library dependency upgrades, why would one use Ubuntu packages versus .deb files you could get from the software manufacturers? (e.g. Skype, Eclipse, Opera, etc..)
Could be any number of reasons, depends on the user and source.
Open source. The packages in the Ubuntu repositories are open source. The others you mentioned may be packaged in a .deb, but not open source.
Patches. The kernel comes to mind here, you can download a kernel from several locations, but it may not have the Ubuntu patches.
Compatibility. Just because it is a .deb does not mean it will be compatible with Ubuntu.
Quality. This overlaps with #3 - one can convert a rpm -> deb with alien for example, but where is the quality control ?
Trust - This depends on your personal paranoia threshold. There are users with enough paranoia not to trust even the Ubuntu repositories. Others trust Ubuntu, but not a closed source binary blob.
Support. You will get minimal or no support from Ubuntu on .deb from elsewhere. Less with the closed source blobs (it varies with popularity of the product).
My general advice is that if is in the repositories, you are going to be better off using the Ubuntu repositories.
If not, IMO, you are better off compiling from source. Implied in doing so is at least some cursory review of the code. yes it is unrealistic to expect end users be able to jump in and start reviewing source code, but nothing wrong with getting a start. You will pick up on major problems (the code will not compile) off the bat.
If the source code is not available, and all you have is a .deb it comes down to trust.