It'll probably vary depending on the spell in question. So, I'll limit my response to the dimension door spell which specifically states "caster CAN bring along objects as long as their weight...bla bla bla" Other spells would be up to DM discretion, but I would use the following as a guideline.
What that says to me is that he can choose what gear to bring and what not to bring. Underwear, but not shirt in the epic cannonball example would be fine.
Plus DD is a verbal only spell (still spell not required) so in my mind that's tailor made to get out of grapples, manacles, straight jackets, web, net, or some gigantic creatures trachea.
Now that's just gear. Poisons and effects (such as fire) or parasites would are another matter. As a DM I would rule that you cannot escape flames or poisons simply by teleporting away since they cannot be classified as gear, nor are they in any way under your control.
If you swallow an item on purpose for some clandestine reason I would probably allow DD to be used to retrieve it, but mostly because I don't want to role play an 8-10 hour wait for it to come out naturally. I refuse to do a price check on medieval laxative. I don't run that kind of game.
In summary anything that could be classified as Gear could be teleported or left as desired since it is under casters control anyway. You can get undressed with all the fancy flourish magic has to offer. You'll be the envy of strippers and showgirls everywhere.
Poisons, parasites, chemical reactions, and the like are NOT under your control cannot be selectively left behind. This is not the last season of Star Trek; The Next Generation so not all problems (and solutions for that matter) are caused by a telelporter.
From MY understanding of the 3.5 rules.
Teleporting or DD or even dimensional leaping(eberron) all bring what the caster is wearing. I have never heard of any type of spell except from the Book of Erotic Fantasy that will strip a charecter of their clothes.
That being said if you the DM don't think it's reasonable then by all means do it.
As far as the escapeing from manacles and grapple and the like in my games my DM allows us to do that because your not "wearing" manacles they were put on you, they may be attached but they are part of a larger structure( IE the wall) now the straight jacket is something you are wearing and the spell really can't differentiate between a jacket or your underwear so thats a DM call.
If the mage doing the casting wants to leave something behind that seems reasonable to me. I would make it a all of nothing type deal though because fine manipulation is very hard to do. So if you want to get out of your straight jacket then you do but your pants and underclothes and everything else is where you were not where you end up.
If the player complains that it's unfair just remind them that according to the spell description all items the mage is wearing go with him. Obviously you can't wear a person so getting outta grapple is fine but clothes and straight jackets are a little too much.