Home Depot has a program called "Pro Xtra" that will work with any credit or debit card, not just their own store card. When you sign up for it, you give them the numbers of the cards you want to use with it. After that, whenever you buy anything with those cards at HD, that receipt will show up on your Pro Xtra account on their site. It's possible to assign an identifier to each receipt on their site, but I don't know if their site lets you split receipts. The web site will also break down your total spending by what they consider the item categories to be (lumber, paint, flooring, electrical, plumbing, etc), which might be interesting. If I remember correctly, you can also download some of the data as a CSV, so you can more easily pull it into a spreadsheet.
Pro Xtra also has a feature where if you spend more than $5000 a year (I think), you get some cash back. They keep track of it over two six-months periods.
When I had it, it was because I was a member of the local REIA; I don't know if it's possible for people off the street to sign up for it, or if it's free to sign up.
I think there's a version with less features, just called Pro, that may be free - I don't know how much functionality you get with it, though. I think HD has relatively recently changed the feature sets of each program, so it's probably a good idea to check their site, or ask at the "pro/contractor" desk at HD when they're not too busy.
I'll add my voice to the chorus endorsing @Bob H.'s idea of "do it as you go". When I first rehabbed a house, I kept all the receipts, but I didn't punch them in for a while. When I went to do my taxes, I had to spend a long time doing data entry, sorting expenses into the various tax categories, trying to figure out what some cryptic item was on a receipt, etc. I got it done, but from then on, I tried not to let the receipts age more than a couple of days before I put them in the computer.
I still just use spreadsheets to keep track of things. On my "receipts" spreadsheet, each receipt has its own line. I enter the total, and then I have several columns for the various tax categories. If the receipt all goes in one category, I just put it there; if not, I split up the items (and the sales tax) into the various categories. I have a formula on each line that adds up all the categories on that line, compares it to the receipt total on that line, and prints "ok" if it adds up, or "ng" if it doesn't - this provides a check on my work of splitting it up. Usually I mess up when rounding the sales tax.
You might be able to do a similar thing with houses; at the top level, each receipt goes on a line, with columns to the right for "123 Main", "456 Oak", etc. Split the receipt among the different houses. Then, have another spreadsheet or tab for each house, where you take the amount from the top level, and split it up among the tax categories. (This is starting to be complex enough that using real, official accounting software might be a better idea.)
Another thing I do on the receipt spreadsheet: when I get my bank and credit card statements at the end of the month, I go through the spreadsheet and bold all the receipt totals that are on the statements. Every once in a while, this helps me find a receipt I forgot to key in, which is usually either lurking in my wallet or still in the bag from the store.
Something to ask your accountant or tax person about: when you get cash back on the credit card for a business purchase, do you need to credit that cash back to your business? I do it on mine, but that's mostly because I only use my cash-back credit card for a few relatively large purchases. For smaller purchases, I just use my business debit card.
One further piece of advice - if you use any kind of online record-keeping, make sure you occasionally make a local copy of the data. Often there is a way to download an Excel, CSV, zip file, or some other kind of file that you can keep on your PC at home. You probably don't have to do this every day, but do it at least once a month. This is to guard against the online service getting hacked, going out of business, or trying to start charging you $500 a month to get at your own data. If you have a local copy of the data, you probably can get enough information out of that to do your taxes.
