I have several recommendations below in regards to instruments and software. It might be a little technical (as a composer I am a MIDI enthusiast), but on the bright side it'll likely sound much better than resorting to Mario Paint Composer.
Instruments:I noticed that the Edirol Hyper Canvas provides some of the sounds in ZUN works (eg. the power kit in Sakuya's EoSD theme) and offers plenty of options to tweak the instruments (ZUN trumpets are simple to make with a few MIDI parameter changes). Catch is that it only has 256 instruments and 9 drumsets (enough to cover the GM2 standard), but a far cry from the SD-90's 1050 instruments and 30 drumsets (which also supports GS and XGLite).
It is discontinued, however, and finding it may be difficult (nor can I help with this). Also I have no idea how well it runs on Vista and 7, for I use it with other MIDI VSTis (Edirol VSC-MP1, Yamaha S-YXG50, and a converted S-YXG2006LE) in an XP virtual machine.
Another hardware option is the Roland SD-50, which has a few more instruments and can be run off USB. It is quite expensive ($400), but due to its recent release most current audio software on Windows and Mac will support it.
EDIT: Also note Bigode's post below on the SD-50 and SD-90's sounds.
As for guitars, I use a couple guitar soundfonts or Logic software instruments, depending on the style of mix I am trying to do.
DAW Software:I use them in conjunction with OpenMPT, but tweak the MIDIs a bit in Anvil Studio and Synthfont (OpenMPT's MIDI handling is quite terrible). Mixing the audio tracks as well as remixing of the MIDIs are done in Logic Pro.
ZUN used Cubase SX according to the BAiJR interview. Then again, this was back in 2005 so he probably upgraded between then and now.