Word Order in Japanese

This is one reason particles are so handy. As long as every part of the sentence is properly marked with particles (where needed), any part can go anywhere as long each part remains intact and the verb goes at the end of the sentence. Even the "verb at the end" rule is sometimes broken in casual speech, though usually only for emphasis or when adding afterthoughts. Generally speaking, the later in the sentence something appears, the more important it is. In any case, all of the following examples are perfectly legitimate (though some are unlikely or even awkward) and while they may put different amounts of weight on the different parts of the statement, all mean the same thing: "I will eat breakfast at nine o'clock tomorrow."

And that's not even taking into account the possibility of also listing where, with who, or other potential details. Generally speaking, the ordering tends to be approximately: topic, time, place, indirect object, direct object, and the verb of course coming last. However, there are no fixed rules. In casual speech, things may even come after the verb.

Noun Modification

Phrases and words that modify nouns come before the noun they modify. In English, qualifying phrases normally come after the noun while adjectives come before. Japanese places both before the noun. In Japanese, the qualifying phrase can be as simple as a brief adjective or as complicated as a full sentence.

If the modifier ends in a short form verb or -i adjective, simply place it before the noun, using the appropriate short form congugation with no further changes. Verbs and -i adjectives used to conjugate differently for this (attributive form) than when ending a sentence (conclusive form), but the distinction is now obsolete and only appears in old or poetic text.

Modifiers that end in a -na adjective or noun vary. A phrase in negative and/or past form will end in a form of the copula, which resembles a verb and acts as described above.

Otherwise, it's a bit different. For -na adjectives, add な (na) between the adjective and the noun (this is why they're called that).

For ordinary nouns, add の (no) in most cases...

...however, sometimes the noun being described is the noun describing it, but using の may suggest a different meaning. In these cases, である (de aru) more clearly expresses the intended meaning. Here's an example from Chrono Trigger:

Significantly different meanings could be taken from it if she had used の instead of である:

The first meaning remains possible, but less obvious without proper context. Using である rather than の here makes it unambiguous.

Classical Japanese conjugations

I've added a more detailed section on classical (archaic) conjugations since writing this, but here's a brief summary:

Many verbs were the same either at the end of a sentence or before a noun, while a few ended in ～り (-ri) when finishing a sentence and ～る (-ru) before a noun, and still others would add a ～る (-ru) when before a noun that was absent when finishing a sentence. Examples: 人がここにあり (hito ga koko ni ari) vs. ここにある人 (koko ni aru hito), 滴が落つ (shizuku ga otsu) vs. 落つる滴 (otsuru shizuku). The last type also led to certain verbs ending in a doubled る when used before nouns, as in 流るる川 (nagaruru kawa).

For -i adjectives, one group that now ends in ～しい (-shii) was ～し (-shi) at the end of a sentence or ～しき (-shiki) before a noun, while the other group was ～し (-shi) at the end of a sentence or ～き (-ki) before a noun. Examples: 太陽が美し (taiyou ga utsukushi) vs. 美しき太陽 (utsukushiki taiyou), 道が長し (michi ga nagashi) vs. 長き道 (nagaki michi).

-na adjectives and nouns (usually) used にある (ni aru), or its contracted form なる (naru), to connect, instead of the modern な (na) for adjectives and の (no) for nouns. Examples: 古川が学者なり (Furukawa ga gakusha nari) vs. 学者なる古川 (gakusha naru Furukawa), 人間が愚かなり (ningen ga oroka nari) vs. 愚かなる人間 (oroka naru ningen). Certain words instead used とある (to aru) or its contracted form たる (taru), but while many of the なる adjectives have survived as な adjectives—and a few, like 単なる (tan naru), still exist with the なる intact and act as set phrases that exclusively modify nouns—the たる class has almost entirely died out. 堂々 (doudou), a relatively common straggler, has the adjectival form 堂々たる (doudou taru) and the adverbial form 堂々と (doudou to).

Though I'm not sure whether it's directly related, たる can also be used with nouns, sometimes even in the modern language. It has more to do with having the proper qualities of something than simply being that in name. So, for example, while 学生なる者 (gakusei naru mono)—or 学生である者 (gakusei de aru mono) in slightly more modern language—refers to someone who is a student, 学生たる者 (gakusei taru mono) refers to one who demonstrates the proper responsibilities and behaviors of a good student.

Particle Placement

Particles need to come directly after the word or phrase that they modify, otherwise it's impossible to tell what they're supposed to be doing. This is particularly important to remember with particles that are frequently translated as though they were words, like も (mo), often rendered as "also" or "too", and から (kara), similar to "because", "from", or "since" depending on context. For example, English allows both of the following:

However, in Japanese, while this is correct...

...the following is not correct:

That actually says that Mary speaks English, and that Robert speaks English in addition to some other language.

This sentence is even worse:

I'm not sure what (if anything) that would mean to a Japanese speaker, but it's certainly not likely to be the intended meaning.