I use Google's spreadsheets. I can call on =GOOGLEFINANCE("VTI", "price") in any cell of the spreadsheet to get the (delayed) price of an ETF or mutual fund. I track the number of shares by hand, and when you multiply those together you get the value of each holding.
It's nice having a summary of assets by percentage (stocks, bonds, cash). I track the target percentage for each fund, and at one point created a sheet (one of many in a spreadsheet document) that tracks re-balancing for me. So if Total Stock gained ground maybe it suggests to sell some of that and buy some Total Bond.
I'd suggest starting a spreadsheet from scratch, and at least add up all your stock funds to get your amount of stocks.. all the bond funds for allocation to bonds.. and then calculate the percentage of each. That gives you the most basic picture of your assets, and can help decide when re-balancing is needed.