Most of the guidelines and checklists available on the internet are for "web usability" is there any checklist for "software usability"?
usability is best evaluated by watching a set of representative users try to perform specific tasks
see useit.com for more info, checklists, articles, et al. Usability is a big topic.
There is a book by Larry Constantine about usability guidelines.
I did not read the book (it's on my wishlist), but I saw him at a conference, and the principles he proposed seem sound and efficient. (I don't know if the book talks about usability inspections - his conference did)
Constantine's website, with a bunch of free articles
Web apps are still software. If you mean web vs desktop - I would say there is a huge overlap between what makes a web app useable and what makes a desktop app useable. Fonts, colours, layout, idioms, text (copy), workflow, use of images/icons etc it is the same issues for both. But the key in both cases is to try and see the app through your user's eyes.