If you like to keep track of all your financial instruments in one program, Quicken goes a long way in meeting that need. However, it can be a little tricky to set up a new instrument such as BitCoin (or physical metals for that matter).
Recently, I started accumulating BitCoin and setup my Quicken to track my purchases and their value. Here's how you can setup your Quicken (and likely other PFM software).
1) Add a new account - the important thing to do here is to setup a Brokerage account under Investing, not a Cash or other type of Spending account. While BTC has properties like Cash - to Quicken it looks like a security.
a) Enter the name of your Brokerage - eg BitCoin. Quicken will try to look up a brokerage but obviously won't find one. So just go with your manually entered name
b) Enter a cash balance and statement date as you might with any brokerage. If you are just getting started with BitCoin, set the date to just before your first purchase and your Cash balance to $0
c) When prompted for securities in the account, add a ticker symbol such as BTC$ (Quicken can't parse the bahtcoin symbol). Again, Quicken will try to look up and fail. Add it manually.
d) Indicate your number of coins. Again, if you are just getting started, put this at 0. We'll add them in later. If prompted, answer No to this being a single mutual fund account.
2) Transfer money into your brokerage account - now for each purchase that make of BTC transfer from the account you purchased with into your Brokerage cash account. This is easy if you used PayPal and are tracking that account also in Quicken. You probably have the PayPal side of the transaction downloaded. Just make it a transfer into your BitCoin account. If you go through LibertyReserve, Dwolla, MoneyBookers, etc. into mt gox or other, just track the cash from your bank account into those accounts as though they are transferring to your BitCoin brokerage.
3) Buy "shares" of BTC - enter the transactions from whatever source where you purchased BTC. Each entry will ask for a share price and number purchased. Pretty straightforward there. You can go into the properties of the BitCoin security and add current pricing since downloads from mt. gox are probably not coming any time soon.
4) Analyze your portfolio - Setup in this fashion you can track the value and cost basis of your BTC.
If you play any games of chance, like Double Trouble:http://forum.bitcoin.org/index.php?topic=12096.0
that could generate additional BTC in your portfolio without a purchase per se, you can track the winning using the ReinvDiv entry. Just enter the number of shares gained in the ReinvDiv transaction and it will increase your holdings without adjusting your cost basis.
If you start accumulating "Cash" in your Brokerage due to not having a clear tracking of fees. You can do a MiscExp and track with whatever category you may use. For example, I have a Bank Fee category that I use for such fees.
Hope this helps!