A few general apps you might find useful:
Emit: Allows you to stream media from your PC/Mac to the Nexus. I tried various other products and found Emit to be the one that worked best and wasn't burdened with too much fluff. It works much like Air Video on iOS, which I had wanted to find an equivalent for. I use this to stream movies to the Nexus while couch-potatoing.
Kingsoft Office: A full office suit that is entirely free and without ads. I don't know how they do it, but it's full featured and costs nothing. I don't do much work on the Nexus (not until I get a keyboard for it), but it's good enough for quickly dealing with a document when and if Google Docs isn't available.
AppSales: An app that notifies you of sales of popular apps on the store. It can be configured to meet your individual needs. It even has a watch list. I mostly use this to learn of sales of games that I might enjoy, and I set it to only show popular stuff, so it's just a few entries per day. Sales are often very short-termed (a day or two), so this is a good way for me to not miss out on good deals.
Avast: A free anti-virus suit that sits in the background and keeps your system secure. Unlike iOS, Android is a somewhat easy target for malware, so while I'm usually not all that fond of anti-virus software and think it's often a waste of system resources, in this case I'd recommend it. It has some additional features that you can subscribe to, but they are not necessary. All alternatives I looked into were either expensive or sucked. Avast has a good reputation in the Windows world, too.
AdBlock Plus: Google took this out of the store earlier in the year, but you can still get it from the developers' own site. It makes web browsing faster and frees up some screen real estate.
Available here. (This will require you to temporarily enable downloading of apps from third party sources; you can turn it off again when you have Adblock installed.)
Dropbox: I'm not a huge fan of cloud storage, but I use some "notes" text files on all of my devices for writing down story ideas or whatever else pops up on my mind that I don't want to forget, and Dropbox is the way to keep those text files updated on all systems. There are other ways to do this, but I like it simple.
For reading, I use the already mentioned
Calibre Companion and
Moon+ Pro. Both are very much worth the few dollars they cost. The other, above listed apps are all free, except for Emit.