Information on how to correctly make sprite textures is just not on the web anywhere. There are so many subtle problems with making transparent textures for use in a 3D engine, here are some of the things I learned recently from my hobby project:

Generally the easiest way is to paint on a transparent background, that is, don't try and paint the alpha channel yourself. That's because it's a complete nightmare trying to match up your rgb and alpha channels correctly. This is one of the reasons why you see loads of games with dark 'halo's around their particle textures (although it's not the only reason). Unless you want to get really tricky and try and paint your own pre-multiplied texture it's not worth it, just create a new image in Photoshop with a transparent background and export as PNG.

Note: the Photoshop Targa exporter won't export the alpha channel properly from a transparent image, it only supports alpha if you explicitly add the alpha channel to an RGB image and paint it yourself. This is a slight pain because I've always favoured Targa as an image file format that's easy to read / write but in this case Photoshop drops the ball once again.

OK now you have your image exported, the image is currently NOT pre-multiplied, it may look like it in Photoshop and most image viewers but on disc it is not pre-multiplied.

Read the file into ram using libPNG or your PNG library of choice.

Generate mip maps... this is where it gets interesting. If you just call something like gluBuild2DMipmaps() your texture will be wrong, the lower level mipmaps will have a dark halo around the edges. Now what most artists do in this case is convert it to a non-transparent image and start painting in some bright colour around the edges of their sprite in the RGB channels, this is the equivalent of a really nasty filthy hack from which no good can come. You can never paint just the right colour in there and can never get it in just the right place, if you're having this problem go talk to your coders and get them to implement a better texture import pipeline (see below):

The fix is really quite simple and you should probably have already guessed that it is to use pre-multiplied alpha. If you haven't heard of it before read here:

Tom Forsyth's blog

http://keithp.com/~keithp/porterduff/

Although it's not mentioned on those sites pre-multiplication is also the solution to building mipmaps correctly. Let's imagine you don't pre-multiply before you downscale to build your mipmap, you have four source RGBA texels from the higher level:

t1, t2, t3, t4

In some kind of box filter arrangement, then your destination pixel in the next lower mip is computed like this:

lowermip.rgb = (t1.rgb + t2.rgb + t3.rgb + t4.rgb) / 4
lowermip.a = (t1.a + t2.a + t3.a + t4.a) /4

And when you come to render with your blend function set to GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA you get:

framebuffer.rgb = lowermip.rgb * lowermip.a + framebuffer.rgb * (1.0-lowermip.a)

It should be farily obvious why this doesn't work, the filtered RGB channel will contain information from neighbouring pixels even if those pixels have a zero alpha. As the background in most exported source textures is black it's the equivalent of 'pulling in' black to your lower mip rgb channel.

The very simple solution is to use pre-multiplication which makes your lower mip calculation like this:

lowermip.rgb = (t1.rgb*t1.a + t2.rgb*t2.a + t3.rgb*t3.a + t4.rgb*t4.a) / 4;
lowermip.a =  (t1.a + t2.a + t3.a + t4.a) / 4;

So now you're weighting each pixels contribution to your lower mip by the appropriate alpha value. And when you render you set your blend modes to GL_ONE, GL_INV_SRC_ALPHA. Not only do your mips work correctly you can now 'mix' additive and subtractive blending which is great for fire turning into smoke for instance (see references below).

You don't need to export your image pre-multiplied, I fix mine up at import / asset cooking time which is probably preferable so you can keep working on the PNG source asset in a convenient way.

This is really just the basics and mip-map filtering has had a lot of other good stuff written about it:

http://number-none.com/product/Mipmapping,%20Part%201/index.html
http://number-none.com/product/Mipmapping,%20Part%202/index.html

Also see http://code.google.com/p/nvidia-texture-tools/ for some image manipulation source code (the Nvidia Photoshop DDS plugin also has an option to modulate your image by alpha when generating mip-maps).

This is a great little paper about soft-edged particles and pre-multiplied alpha (even though it's not referred too as such)
Soft Edges and Burning Things: Enhanced Real-Time Rendering of Particle Systems