The first, and often repeated, fact is that there are'nt any really bad DSLRs amongst those released in the past 2 or 3 years - it tends to be a case of which has the features you really want, which handles best for you and which make has the best lens selection for future buying.
I've actually used the Nikon models you mention - the D90 might be the oldest but for me is still the best. Don't be put off by its meagre mp - it is a camera you would'nt quickly outgrow and has the advantage over the other 2 of having in body af motor - loads more lenses will af on the D90 over the D5000 or D3100. I was a bit disappointed by the D5000 - not quite sure why. The D3100 is small, great image quality and easy to use - annoying way of moving the af point though.
If I was going for a cheap s/hand Canon I'd try for a 40D,again from personal use - you do sometimes see them about at a reasonable cost.
I should really recommend Pentax as I'm now using one but I don'tn know too much about the other models they do. K-X has a great reputation for image quality though. These days the Olympus DSLR system could be thought of as a bit of a dead end but they do make good well featured cameras and their kit lenses are among the best you can get. No idea about Sony - never been tempted!
So, from your list .... D90