first thing i'd do is actually manually collate everything into one file/folder. Now obviously, you'll need a bit more of a system than just bung it all in one place so you need to decide on a organisation scheme. There are lots of different ways of doing this, the one i've described below is only one way.
On my windows machine i've a folder for pictures. Within this there are a number of folders, one for each year. Within the year, there are months, within months there are folders by day (numbered YYYY-MM-DD so that they'll stay in date order). Every time you move your files onto the computer, go into the appropriate month, create a folder with the current day, and copy the files from the SD card (or whatever) into the folder. It really is a situation where a little organisation at the start pays massive dividends. Sadly, you've already got a bit of a mess to sort out, but the inital hassle of shifting stuff about will be worth it in the end.
All this can be done with the inbuilt facilities of the operating system, and doesn't really need additional software.
I have to confess that I use lightroom to catalogue my photo collection, but even this heavyweight program is easier to use with all the shots under a single directory.
