The hitboxes are smaller than the image of the bullet generally is. This is also true for your hitbox. For very fancy looking bullets (butterflies, knives), the only part with a hitbox is the glowing ball in the middle. Well, technically, this is true for most bullets- but it's especially true for those.
Bubble bullets after EoSD (So, starting in PCB) have a hitbox -much- smaller than the graphic. It doesn't start until around the colored area towards the middle. In EoSD though, whilst it's still smaller than the image, it's much larger than in later games, so be careful. I think these bullets were mostly phased out in favor of generic big-ball bullets after UFO, though... (so, starting with Ten Desires, and maybe Double Spoiler as well) Kind of a downgrade but oh well.
In IN, lasers are... weird. Sometimes you can literally move through them unscathed, the hitbox doesn't seem to always be active (You will usually be hit though, so uh, don't do it on purpose). Also, keep in mind when the laser is just a thin tracer line, it's not "active" and you can safely go through; it's just a warning there's about to be a laser there.
By the way, here's a collection showing exactly how close you can get to bullets without dying. AFAIK it's pretty much frame-perfect though, one more pixel being death; in real play you should not get -this- close, but it's a good reference.
http://thwiki.cc/%E6%B8%B8%E6%88%8F%E6%94%BB%E7%95%A5/STG%E5%88%A4%E5%AE%9A%E6%95%B0%E6%8D%AE The second set of images is from Th13/14/15, where the algorithm changed and some hitboxes got slightly larger.