I know, these are no official rules but I think it´s worthwhile to consider what Skip Williams wrote on this subject in his Rules of the Game article. According to him you can (even must) assume a different form than your familiar:
You choose a form for yourself and for your familiar or companion. The forms you choose don't have to be the same. In fact, in most cases, they cannot be the same because alter self allows the subject to assume a form of the same type as itself only…
When you share an alter self spell with a familiar or companion, the familiar or companion assumes a form of the same type as its own. While an animal becomes a magical beast upon becoming a familiar, such a creature must assume the form of an animal when sharing an alter self spell. For example, a cat familiar is a magical beast; when it shares an alter self spell, it assumes the form of an animal, such as a dog, a bird or a bat, not the form of a magical beast.
The 2nd-level Sor/Wiz spell alter self [trans] (Player's Handbook (2012) 197), in part, says
When the change occurs, your equipment, if any, either remains worn or held by the new form (if it is capable of wearing or holding the item), or melds into the new form and becomes nonfunctional. When you revert to your true form, any objects previously melded into the new form reappear in the same location on your body they previously occupied and are once again functional. Any new items you wore in the assumed form and can’t wear in your normal form fall off and land at your feet; any that you could wear in either form or carry in a body part common to both forms at the time of reversion are still held in the same way. Any part of the body or piece of equipment that is separated from the whole reverts to its true form.
The spell alter self makes no mention of changing the size of equipment like, for example, the spell enlarge person [trans] (PH 226–7) does. (This 2004 Rules of the Game Web column predates many of the revisions that would occur later to spells that change form; look upon its advice and rulings, as always, with a jaundiced eye.) Keep in mind, though, that usually magic items that are worn change size to match their wearer's size.
Mundane outfits like an entertainer's outfit (PH 129, 131) (3 gp; 4 lbs.)—like a backpack, winter blanket, and a day's worth of trail rations—have different weights (and, presumably, by extension, sizes) for Small creatures. This DM has always extended this to mean that such things must be purchased to scale. To compute prices and weights, this DM uses, if the item's worn, the rules for bigger and littler armor (PH 123) and, for other items, the rules for bigger and littler weapons (Rules Compendium 152).
Thus, this DM would rule that a gnome wearing a mundane Small entertainer's outfit that used the spell alter self to assume the form of a human would see that entertainer's outfit meld with his new form because his new Medium human form isn't capable of wearing a Small entertainer's outfit.
So, yes, like one of those nightmares, that gnome-now-human, had he not planned for this eventuality, would be on stage naked.
Keep in mind that the spell alter self et al. are exceptions. Normally, a spell of the subschool polymorph affects gear as follows:
Any gear worn or carried by the target melds into the new form and becomes nonfunctional. When the target reverts to its true form, any objects previously melded into the new form reappear in the same location on its body they previously occupied and are once again functional. Any new items worn in the assumed form fall off and land at the target's feet. (Player's Handbook (2012) 320)
Given this ruling's provenance—in, perhaps, among the last books that'll ever be officially published for 3.5e—, this is likely the final word on spells of the subschool polymorph.
Best Answer
Defining Polymorph's Text
The first point of confusion with the spell Polymorph is clarifying how exactly its text interacts with that of Alter Self. To that end, below is the combination of the two spells as if Polymorph was written as an independent spell instead of a derivative one. This was achieved by breaking both spells down line-by-line, then replacing lines from Alter Self with the respective lines from Polymorph, plus changing lines from Alter Self to refer to "subject/it" instead of "you/your" as-appropriate.
Polymorph begins with the line, "This spell functions like alter self, except that . . .." Typically, there are two separate ideologies for how to interpret this statement: "replaces" and "adds or replaces." For the former, it is assumed that any single element of Alter Self affected by a rule from Polymorph is completely stripped out and fully replaced by the new rules. For the latter, it is assumed that language from Polymorph is simply added to Alter Self unless an acute conflict is created, in which case only the conflicting language is removed from Alter Self.
This answer uses the "replaces" interpretation of Polymorph vs. Alter Self instead of the "adds or replaces" interpretation. The "adds or replaces" interpretation leads to strange rules that do not make much sense from the perspective of a player such as arbitrarily limiting a normally-Fine-sized creature, of which there are no standard player races, from becoming even smaller but otherwise not affecting size choices. So in all cases where a Polymorph rule relates to something directly ruled by Alter Self, the relevant Alter Self language has been discarded completely and replaced by the language found in Polymorph.
Transmutation
Level: Sor/Wiz 4
Components: V, S, M
Casting Time: 1 standard action
Range: Touch
Target: Willing living creature touched
Duration: 1 min./level (D)
Saving Throw: None
Spell Resistance: No
Examining the Rules
With the spell defined more-clearly, we can now go section-by-section to determine exactly what Polymorph really does, arranged by paragraph:
Choosing a Legal Form:
Effect on Subject Hit Points, Attributes, and Stats
Effect on Subject Special Abilities
Effect on Subject Speaking and Spell-Casting
Effect on Subject Physical Qualities
Effect on Subject's Type
Effect on Subject's Appearance
Effect on Subject's Equipment