1. Hand-picked grain, divided by collection centre. The answer is SELECTED. The definition is "Hand-picked". This word is also SEED ("grain") containing ("divided by") LECT which is the middle four letters ("centre") of "collection": SE-LECT-ED.

5. Makes the same pitiful squeal. The answer is EQUALS. The definition is "Makes the same". This word is also an anagram ("pitiful") version of SQUEAL.

10. To stay alive, leave around the beginning of September. The answer is EXIST. The definition is "To stay alive". This word is also EXIT ("leave") containing ("around") the letter S, which is the first letter ("beginning") of September: EXI-S-T.

11. Spar in ring with Eärendil, for example. The answer is TRAVELLER. The definition is "Eärendil, for example". This word is also the same as (appears "with") a nautical term, "traveller" for a metal ring that moves on a spar, or the spar itself ("spar in ring").

12. Point toward the West in expression of joy and bounty. The answer is ABUNDANCE. The definition is "bounty". This word is also BUN, which is NUB (the "point", as of a story) spelled backwards (i.e., the letters arranged from the East, or right, "toward the West", or left) in A DANCE (an "expression of joy"): A-BUN-DANCE.

13. Elvish was my bastion against the ravages of time. The answer is NENYA. The definition is "bastion against the ravages of time" (the primary function of the Elvish rings was to slow down time). This word is also NE (Quenya, or Elvish, for "was") plus NYA (the Quenya suffix meaning "my").

14. Approaches crooked lanes around Bag End. The answer is ANGLES. The definition is "approaches", as a noun. This word is also ANLES, an anagram (or "crooked" version) of "lanes", containing ("around") the letter G, which is the last letter (or "end") of the word "bag": AN-G-LES.

15. Weakest subject frequently is Latin. The answer is SOFTEST. The definition is "Weakest". This word is also S (abbreviation for "subject") plus OFT ("frequently") plus EST ("is", in Latin).

18. Make strong Exilic Noldorin past tense. The answer is STIFFEN. The definition is "Make strong". This word is also EN (abbreviation, used by Tolkien, for "Exilic Noldorin") following ("past") STIFF ("tense").

20. Is kept in view. The answer is BEHELD. This word is also BE ("is") followed by HELD ("kept").

22. Elf's ancient parting response. The answer is NOLDO. The definition is "Elf". This word is also OLD ("ancient") in ("parting") NO (a "response"): N-OLD-O. Note that the 's is a contraction for "is", and not a possessive as it might appear to be on casual inspection.

24. Leaders of North and South are hiding in unimportant early city of Gondor. The answer is MINAS ANOR. The definition is "early city of Gondor". This word is also N A S A (the first letters, or "leaders" of the four words "North and South are") in ("hiding in") MINOR ("unimportant"): MI-NASA-NOR.

25. One Ring, done, finished, tossed aside. The answer is ABANDONED. The definition is "tossed aside". This word is also A BAND ("One Ring") followed by ONED, an anagram (or "finished" version) of "done".

26. Wait and ask between the middle of May and the end of June. The answer is ABIDE. This is also BID ("ask") between A (the "middle" letter of the word "May") and E (the final letter, or "end of June"): A-BID-E.

27. Skip out with just what you have coming. The answer is DESERT. There are two definitions: "with just", i.e. as in "just desert" it means "what you have coming". It also means "skip out".

28. Note about trail seen in certain phase of moon. The answer is CRESCENT. The definition is "certain phase of moon". The following words can be "seen in" this word: C (a "note"), RE (abbreviation for "about"), and SCENT (a "trail").

Down

1. Let's fall over like old monuments. The answer is STELAS. The definition is "old monuments". This word is also STEL (a backwards version, or "fall" of "let's") followed by ("over", since this is a Down clue) AS ("like").

2. Alas, someone High-Elven died embraced by fifty-one woodelves. The answer is LAIQUENDI. The definition is "woodelves". This word is also AI (High-Elven, or Quenya, for "Alas") followed by QUEN (Quenya for "someone") followed by D (abbreviation for "died"), contained in LI (Roman numeral for "fifty-one"): L-AI-QUEN-D-I.

3. Unhinged facing door led to inner circle of Minas Tirith. The answer is CITADEL OF GONDOR. The definition is "inner circle of Minas Tirith". This phrase is also an anagram ("unhinged" version) of "facing door led to".

4. Nesting nuts?! The answer is ENTINGS. The definition is "Nesting nuts?". This word is also an anagram ("nuts" version) of "Nesting".

6. First Lady often has request poorly executed. The answer is QUEEN OF THE STARS. The definition is "First Lady". This word is also an anagram ("poorly executed" version) of "often has request".

7. Elvish pool and stars. The answer is AELIN. The definition is "Elvish pool". This word is also A (the Sindarin, or "Elvish" word for "and") followed by ELIN (the Sindarin word for "stars").

8. Help with unresolved state of difficulty up around front line. The answer is SERVANTS. The definition is "Help". This word is also (appears "with") SERTS, which is STRESS ("state of difficulty"), but unfinished ("unresolved") and written bottom-to-top ("up"); containing ("around") VAN ("front line" of battle): SER-VAN-TS.

9. Crebain almost never up from South. The answer is RAVENS. The definition is "Crebain". This word is also NEVAR ("almost", but not quite, "never") written from bottom to top ("up") on top of ("from") S (abbreviation for "South").

16. Took wife a rose. The answer is EGLANTINE. There are two definitions: "Took wife" (Eglantine Banks married Paladin Took, and therefore was a Took wife. She was Pippin's mother.) and "a rose".

17. Digs near ruinous remote outpost of Gondor. The answer is ISENGARD. The definition is "remote outpost of Gondor". This word is also an anagram ("ruinous" version) of "Digs near".

19. Appointment with one of the big folk up in the capital of Gondor. The answer is NAMING. The definition is "Appointment". This answer is also (appears "with") NAM, which is MAN ("one of the big folk") written backwards (or since this is a Down clue, written "up") followed by IN and then G (the first letter, or "capital" of Gondor).

20. Room on Arda, marred, for Elvish bastard? The answer is BEN-ADAR. The definition is "Elvish bastard?" (BEN-ADAR means "without father" in Sindarin). This word is also BEN (a Scottish dialectal word for a kind of "room") followed by (or since this is a Down clue, "on") ADAR, an anagram (or "marred" version) of "Arda".

21. Shining silver generally found in Middle-earth. The answer is ARGENT. The definition is "Shining silver". This word is also GEN (abbreviation for "generally") in ("found in") ART the "Middle" letters of "earth": AR-GEN-T.