I also wanted to mention that you can get a lot of information about a particular yarn on the manufacturer's website. Useful if a pattern just gives the name of the yarn. Then once you have the gauge, you can go looking at other brands' sites for similar weight yarns before you buy at an online retailer or your lys.
Proportions/percentages: That's a great help Carie! I've been doing this myself, but I didn't mention it because sometimes one just wants a "straight-across" substitution.
Right now, I'm using the same yarn a pattern calls for, but I CANNOT get gauge, no matter how much I vary my tension or needles. So, I made sure to get one dimension and adjusted for the other using proportion. I haven't tried percentage adjustment for both dimensions yet. I imagine it may not work if the percentages are different. And yes, I think those knitting applications do precisely the same thing - didn't know there was freeware...going to look...
WIP: GAAA for m&d, purse for grandma (needs assembly), Grannie Smith Cardi (still), 3 quilts, maybe five
In the Wings: felted clogs, socks
Recent FO: dishcloth for swap, booties for cousins babe
KALs: Grannie Smith, Monthly Dishcloths, Mason-Dixon