Help me improve my dismal musical ability!

As far as making chord changes that sound good, it's all about The Circle Of Fifths (a quick search on google will pull it up). As long as you know your I, vi, IV and V chords in a key (the 1, minor 6, 4 and 5 chords, respectively), you'll be able to make some decent songs, and play a ton of already made ones. Try that out, as far as software I don't really have any recommendations, though. Something with basic backing tracks so you can play along, is probably what you're looking for. Good luck :)

Back in college we had to use MacGamut for ear training. It covered chords and inversions, intervals harmonic and melodic, and possibly melodies too. It played the whatever in question (only a certain number of times, at the later advanced levels) and you could either notate with the mouse or use a (musical, electronic) keyboard hooked up to the computer. We might have had to notate modulations too, but I don't remember clearly. All this to say that it's not exactly what you're looking for, but it might help. The software we used was for Mac, but there might be a Windows version. Google around and maybe you can find it! (and let me know if you do...miss those long, long hours at the music lab getting them stupid chords right)

This might be way below your level, but worth a shot: ear training games called https://trainer.thetamusic.com/en/content/getting-started

Btw the PurelyPiano site lets you download PDFs and listen to all of its exercise content for free online, as long as it's for personal use. Just click on the Content List links at the bottom.

I actually wrote a piece of commercial software for practicing against other people's music - it's called http://slowgold.com. I'm not sure that it's really what you're looking for - to be honest, I believe 90% of our customers are people practicing Pink Floyd licks and the like - but check it out and if you like it I'll cut you a monster deal on it (memail me). Honestly, the way I do it is to go back to the fundamentals. When I pick up my instrument after a long delay, I tend to do major, minor, harmonic, and whole tone scales - and major, minor, major 7th and minor 7th and diminished arpeggios - in all 12 keys. I can't do them all perfectly, but I can do them all, and that alone makes my fingers more happy. I also take well-known pieces and transpose them to "difficult" keys (SlowGold is good for that too). When I find something that's particularly hard, I might write something in that key, scale, or whatever, just for me to practice against.

If you've got an XBox or PS3, it might be worth getting Rock Band 3 and the keyboard peripheral. http://www.amazon.com/exec/obidos/ASIN/B003RRTWSE/metafilter-20/ref=nosim/, and the keyboard is a surprisingly solid two-octave MIDI keyboard. It won't teach you much beyond how to play the keyboard parts for the songs on disc, but there's a wide selection, it's fun, and it's cheap.