I chose the Rough Guide as it was more up-to-date than the Lonely Planet (ok, only by a month which probably makes no difference at all) and I'd used the Lonely Planet last time and fancied a change. Whilst in Reykjavik I looked at other people's copies of the more recent Lonely Planet.
I usually like Rough Guides, but have to say that I wasn't too impressed with this one. It seemed to be lacking information. Places I knew were in the Lonely Planet and just wanted to check my book for the address, couldn't be found in the Rough Guide. This would have been ok if there'd been alternative places in the Rough Guide, but there didn't seem to be. Also I noticed a few mistakes. For example, the Rough Guide refers to the Downtown Hostel as the City Hostel, and the City Hostel as the Reykjavik Hostel.
When I looked at the more recent Lonely Planet it seemed just as good as the older one I had at home. I didn't need to use the Rough Guide for travelling around the country, but my impression is that it wouldn't have been as good as the Lonely Planet for this either. So it's not that the lesser Reykjavik section is balanced out by a much meatier rest of the country section.
But the best guide book for Reykjavik has to be The Real Iceland by Pall Asgeir Asgeirsson. I bought this whilst I was in Iceland last time and it has lots of quirky information in it, such as the addresses for each of the Sigur Ros band members and the address for Bjork's mum (as well as for Bjork herself, but it warns her son can be bad-tempered if you turn up on the doorstep). It's only a slim little book (so nice and light to carry around) but is really informative and I'd highly recommend anyone heading to Reykjavik to get hold of a copy.