Thistle,
Logos looks like an excellent tool. It is probably the leading PC / MAC based study tool. They even have a iPhone / iPod Touch program that allows you to read your books on your mobile device. No notes or highlighting yet available on the iPhone / iTouch.
Regards your question about Catholic Bible study. Well, it all depends on the software that you purchase from Logos. They sell everything in bundles. The least expensive is about $150 with the next package being $265. You get an amazing amount of material for this. It is well worht it. However, the specific Catholic material is then extra. The NAB is available and the NABRE is coming soon. You will not find the Navarre Bible commentary, Orchard Commentary, Haydock or Ignatius. They are looking at providing the Old Catholic Encyclopedia. There are other Catholic resources. Take a look on their site - search for Catholic. not sure that any of these resources would be my primary choice.
I use OliveTree on my itouch and iPad. They are developing a PC based version - so probably expect that sometime in 2011. They have the NABRE and some great Bible materials - Strongs, Maps, etc. But little additional that is Catholic (they have some early Church Fathers and Augustine). Laridian has an iPhone / iTouch and PC version. Buy the resource once, use it on all your platforms. But again the Catholic element is limited. The NAB (not the NABRE) is about it.
So, wherever you go, if you want specifically Catholic, then you are looking to harcopy books.
Good luck in your search.
Hal.