I think the more important aspect is your sound card, mics, and pre-amps. That will make more of a difference in the quality of your recordings than anything else. The programs all record pretty much the same, just have different levels of editing ability, and interchangeability (is that a word?).
Since it sounds like you would only be doing one instrument at a time, you could get away without a mixer in the chain. Even if you wanted to put two mics on an acoustic, as long as the pre had two channels, you'd still be fine. DBX makes some good pre-amps, and are fairly easy to find used and cheap. I found a Bellari pre-amp used, and have been really happy with it.
As far as mics go, just remember, if you get a condenser mic, you will need to get power to it, which usually is in any mic pre, but you want to check just to make sure.
As far as multitracking programs are concerned, Pro tools is the standard, so any plug-ins will be made for it. Also, if you need to send it anywhere else to work on, they will be able to without any compatability issues.
I just got done recording an album with my friends in my basement. We recorded all the basic tracks onto a Tascam eight track reel, then dumped them down onto a computer to mix and a few overdubs. We used Acid to mix it (the program, not the illicit drug). I liked it a lot. It was fairly intuitative. If you want to see if you like the sounds we get on stuff, go to
http://www.theplasticcontainers.com/pagetwo.html, and see if you want to take any of my advice.
Hell, I'm such a nerd I could talk about recording gear all day. Let me know if this is too much information for you, or if you want more.
Also, I can't stress enough how much I love Tape-Op. Microphone placement techiques, digital vs analog techique, other general recording advice. It's a treasure trove of knowledge.
