If you want good analog I/O, you can wire up ADC and/or DAC chips to the parallel port (hint: for power, use the game port connector or a spare disk drive power connector wired to outside the computer case, unless you have a low-power device and can use the parallel port itself for power, or use an external power supply), or buy an AD/DA card (most of the older/slower ones are controlled by I/O ports). Or, if you're satisfied with 1 or 2 channels, inaccuracy, and (probably) bad zeroing, a cheap sound card supported by the Linux sound driver should do (and it's quite fast).
With accurate analog devices, improper grounding may generate errors in the analog inputs or outputs. If you experience something like this, you could try electrically isolating your device from the computer with optocouplers (on all signals between the computer and your device). Try to get power for the optocouplers from the computer (spare signals on the port may give enough power) to achieve better isolation.
If you're looking for printed circuit board design software for Linux,
there is a free X11 application called Pcb that should do a nice job,
at least if you aren't doing anything very complex. It is included in
many Linux distributions, and available in
ftp://sunsite.unc.edu/pub/Linux/apps/circuits/ (filename
pcb-*).