Officially, bonuses from items worn long-term don't count as permanent.
The D&D 3.5 Player's Handbook p.58, "Experience and Levels", writes:
Use your character's current Intelligence score, including all permanent changes (such as inherent bonuses, ability drains, or an Intelligence increase gained at step 4, above) but not any temporary changes (such as ability damage, or enhancement bonuses gained from spells or magic items, such as a headband of intellect), to determine the number of skill points you gain.
The D&D 3.5 Dungeon Master's Guide p.268, under the Tome of Clear Thought, concurs:
Because the tome of clear thought provides an inherent bonus, the reader will earn extra skill points when she attains a new level (unlike with the benefit provided by a headband of intellect).
The D&D 3.5 FAQ (Jun 30, 2008) explains that temporary bonuses do apply to bonus spells, but you lose them if you lose the benefit of the item, starting with uncast spells (which exact spells you lose are otherwise unspecified):
Do ability enhancing items (such as the headband of intellect, cloak of charisma, and periapt of wisdom) grant bonus spells to the appropriate spellcasters?
Yes, you can get extra bonus spells if you have an item that increases the ability score that governs your spellcasting. To get the extra bonus spells, you must wear the item while resting to regain spells and all through your initial daily preparations for spellcasting. [...]
If you lose the item, you immediately lose the bonus spell slots the item gave you, starting with any uncast spells you have of the appropriate levels.
For what it's worth, in my 3.5 games I always allowed headband of intellect to increase skill points, including retroactively. However, the rules and the FAQ officially say you can't do this. For non-Intelligence items it doesn't really matter; e.g. if you have an item granting Constitution +2, you gain 1 hit point per level when you put it on, and lose 1 hit point per level if you take it off or its ability is suppressed by an antimagic field or the like.
The D&D 3.0 Player's Handbook p.145 implied that the headband of intellect might grant bonus skill points if worn constantly during the previous level, specifically stating that wearing it for a short time doesn't grant it.