Old English be- (unstressed) or bi (stressed) "near, in, by, during, about," from Proto-Germanic *bi "around, about," in compounds often merely intensive (source also of Old Saxon and Old Frisian bi "by, near," Middle Dutch bie, Dutch bij, German bei "by, at, near," Gothic bi "about"), from PIE *bhi, reduced form of root *ambhi- "around."
As an adverb by c. 1300, "near, close at hand." OED (2nd ed. print) has 38 distinct definitions of it as a preposition. Originally an adverbial particle of place, which sense survives in place names (Whitby, Grimsby, etc., also compare rudesby). Elliptical use for "secondary course" was in Old English (opposed to main, as in byway, also compare by-blow "illegitimate child," 1590s, Middle English loteby "a concubine," from obsolete lote "to lurk, lie hidden"). This also is the sense of the second by in the phrase by the by (1610s). By the way literally means "along the way" (c. 1200), hence "in passing by," used figuratively to introduce a tangential observation ("incidentally") by 1540s.
To swear by something or someone is in Old English, perhaps originally "in the presence of." Phrase by and by (early 14c.) originally meant "one by one," with by apparently denoting succession; modern sense of "before long" is from 1520s. By and large "in all its length and breadth" (1660s) originally was nautical, "sailing to the wind and off it," hence "in one direction then another;" from nautical expression large wind, one that crosses the ship's line in a favorable direction.
Old English fleoge "a fly, winged insect," from Proto-Germanic *fleugon "flying insect" (source also of Old Saxon fleiga, Old Norse fluga, Middle Dutch vlieghe, Dutch vlieg, Old High German flioga, German Fliege "fly"); literally "the flying (insect)" (compare Old English fleogende "flying"), from PIE root *pleu- "to flow," which is also the source of fly (v.1).
Originally any winged insect (moths, gnats, beetles, locusts, hence butterfly, etc.) and long used by farmers and gardeners for any insect parasite. Flies figuratively for "large numbers" of anything is from 1590s. Plural flien (as in oxen, etc.) gradually normalized 13c.-15c. to -s. Fly in the ointment is from Eccles. x:1. Fly on the wall "unseen observer" first recorded 1881. No flies on _____ "no lack of activity or alertness on the part of," is attested by 1866. Meaning "fish-hook dressed to resemble an insect" is from 1580s; Fly-fishing is from 1650s. Fly-catcher "bird which eats insects on the wing" is from 1670s. The fly agaric mushroom (1788) so called because it was used as a poison for flies.
The sense of "a flight, flying" is from mid-15c. From the verb and the notion of "flapping as a wing does" comes the noun sense of "tent flap" (1810), which was extended to "strip of material sewn into a garment as a covering for buttons" or some other purpose (1844). Baseball fly ball attested by 1866. To do something on the fly is 1856, apparently from baseball.
When the catcher sees several fielders running to catch a ball, he should name the one he thinks surest to take it, when the others should not strive to catch the ball on the fly, but only, in case of its being missed, take it on the bound. ["The American Boys Book of Sports and Games," New York, 1864]
late Old English niht (West Saxon neaht, Anglian næht, neht) "the dark part of a day; the night as a unit of time; darkness," also "absence of spiritual illumination, moral darkness, ignorance," from Proto-Germanic *nahts (source also of Old Saxon and Old High German naht, Old Frisian and Dutch nacht, German Nacht, Old Norse natt, Gothic nahts).
The Germanic words are from PIE *nekwt- "night" (source also of Greek nyx "a night," Latin nox, Old Irish nochd, Sanskrit naktam "at night," Lithuanian naktis "night," Old Church Slavonic nosti, Russian noch', Welsh henoid "tonight"), according to Watkins, probably from a verbal root *neg- "to be dark, be night." For spelling with -gh- see fight. The vowel indicates that the modern English word derives from oblique cases (genitive nihte, dative niht).
The fact that the Aryans have a common name for night, but not for day (q.v.), is due to the fact that they reckoned by nights. [Weekley]
Thus in Old English combinations night was "the night before (a certain day or feast day);" compare German Weihnachten "Christmas," literally "holy night." In early times, the day was held to begin at sunset, so Old English monanniht "Monday night" was the night before Monday, or what we would call Sunday night; so saeterniht "Friday night." The Greeks, by contrast, counted their days by mornings.
To work nights preserves the Old English genitive of time. Night soil "excrement" (1770) is so called because it was removed (from cesspools, etc.) after dark. Night train is attested from 1838; night-school from 1520s; night-life "habitual nocturnal carousing" is attested from 1852.
Meaning "go at full speed" is from c. 1300. In reference to flags, 1650s. Transitive sense "cause to move or float in air" (as a flag, kite, etc.) is from 1739; sense of "convey through the air" ("Fly Me to the Moon") is from 1864. Related: Flew; flied (baseball); flown; flying. Slang phrase fly off the handle "lose one's cool" dates from 1825.