I use iGetter as my download program/accelerator. It works really well and has a speed limit if its working _too_ well *cough* speed downloader *cough*
Best of all, when you encounter the whole .php problem, it just goes that one step further and works out what the .php file was linking too. I see it happening heaps, ill download a video and itll come up in iGetter as getfile.php, then it will change to a .mpeg file and will have the name for the video file in the list.
Its shitty coz it asks you to wait for 12 seconds every time you open it unless you buy it. Other than that, it doesnt beg you to buy it and as long as you just keep it going all the time you wont ever have to see the startup window. You get used to it i suppose.
Also, i think there's some hidden little setting that allows you to tell your browser which extensions to play when you click them and which extensions to just download. Dont ask me HOW, but look into it, im sure its there - and if it isnt it should be