Exhibit 10.3

SECOND AMENDMENT

OF

APOGEE ENTERPRISES, INC.

DEFERRED INCENTIVE COMPENSATION PLAN

(2005 Restatement)

The “APOGEE ENTERPRISES, INC. DEFERRED INCENTIVE COMPENSATION PLAN” as adopted by APOGEE ENTERPRISES, INC., a Minnesota corporation, and first effective February 27, 1986, and as amended and restated in a document entitled “Apogee Enterprises, Inc. Deferred Incentive Compensation Plan (2005 Restatement)” effective January 1, 2005 and as amended by a prior amendment is hereby further amended in the following respects:

1. EARNINGS ON THE ACCOUNT. Effective December 31, 2009 for elections made by the Participant for Plan Years beginning on or after January 1, 2010, Section 3.2 of the Plan Statement is amended to read in full as follows:

3.2. Earnings on the Account . The balance of each Participant’s Deferred Compensation Account shall be credited as a book entry with interest, compounded quarter-annually, on the last day of each quarter of each Fiscal Year, or pro-rata for such lesser period as may occur in the event that the Deferred Compensation Account is credited with deferred compensation or reduced by a distribution from the Deferred Compensation Account on a day other than the last day of a Fiscal Year quarter. The applicable interest rate in any Fiscal Year shall be determined as of the beginning of each Fiscal Year and shall be the monthly average yield for the last calendar month of the prior Fiscal Year on United States Treasury securities adjusted to a constant maturity of ten (10) years, as calculated and published by the Federal Reserve Board, or, if the Federal Reserve Board discontinues its publication of such yields, as calculated by such other source, based upon comparable information, as the Committee may select.

2. SAVINGS CLAUSE. Save and except as herein expressly amended, the Plan Statement shall continue in full force and effect.

Exhibit 10.5

FIRST AMENDMENT

OF

APOGEE ENTERPRISES, INC.

2000 EMPLOYEE STOCK PURCHASE PLAN

(Amended and Restated Effective as of May 1, 2003)

The “2000 EMPLOYEE STOCK PURCHASE PLAN,” as adopted by APOGEE ENTERPRISES, INC., a Minnesota corporation, and as amended and restated in a document entitled “Apogee Enterprises, Inc. 2000 Employee Stock Purchase Plan (Amended and Restated Effective as of May 1, 2003),” is hereby amended in the following respects:

1. PURPOSE. Effective February 28, 2009, Section 1.01 of the Plan Statement is amended to read in full as follows:

Section 1.01 Purpose. The purpose of the Plan is to encourage and assist employees of the Company and certain related corporations in acquiring an ownership interest in the Company through the systematic purchase of the Common Stock of the Company under convenient and advantageous terms. It is believed that the Plan will encourage participants to put forth their best efforts toward the profitability of the Company.

2. DEFINITIONS. Effective February 28, 2009, Section 1.03(g) of the Plan Statement is amended to read in full as follows:

(g) “ Current Compensation ” means all regular wage, salary and commission payments paid by the Company or a Participating Affiliate to a Participant in accordance with the terms of his or her employment, but excluding annual bonus payments and all other forms of special compensation.

3. DEFINITIONS. Effective February 28, 2009, Section 1.03(m) of the Plan Statement is amended to read in full as follows:

(m) “ Regular Employee ” means an employee of the Company or a Participating Affiliate as of the first day of a Purchase Period, including a union employee, but excluding an employee whose customary employment is less than 30 hours per week.

4. SAVINGS CLAUSE. Save and except as herein expressly amended, the Plan Statement shall continue in full force and effect.

Exhibit 10.8

SECOND AMENDMENT

OF

APOGEE ENTERPRISES, INC.

PARTNERSHIP PLAN

(2005 Restatement)

The “APOGEE ENTERPRISES, INC. PARTNERSHIP PLAN” as adopted by APOGEE ENTERPRISES, INC., a Minnesota corporation, and first effective June 25, 1987, and as amended and restated in a document entitled “Apogee Enterprises, Inc. Partnership Plan (2005 Restatement)” effective January 1, 2005 and as amended by prior amendment is hereby further amended in the following respects:

1. SHARES SUBJECT TO PLAN. Effective as of the date this Amendment is adopted, Section 6.9 of the Plan Statement is amended to read in full as follows:

6.9. Shares Subject to Plan . Apogee hereby authorizes Two Million Fourteen Thousand (2,014,000) shares of Common Stock to be issued or purchased and designated as Pool A Common Stock pursuant to this Plan. Any Pool A shares that are returned to Apogee by Disqualification may be added to the number of shares available under the Plan for the purpose of funding Pool A.

2. SHARES SUBJECT TO PLAN. Effective as of the date this Amendment is adopted, Section 7.12 of the Plan Statement is amended to read in full as follows:

7.12. Shares Subject to Plan . Apogee hereby authorizes One Million Three Hundred Thirty-One Thousand (1,331,000) shares of Common Stock to be issued or purchased and designated as Pool B Restricted Stock pursuant to the Plan. Any Restricted Stock awarded to Participants that are returned to Apogee by forfeiture or disqualification may be added to the number of shares available under the Plan for the purpose of funding Pool B.

3. SAVINGS CLAUSE. Save and except as herein expressly amended, the Plan Statement shall continue in full force and effect.

Exhibit 10.10

FIRST AMENDMENT

OF

APOGEE ENTERPRISES, INC.

DEFERRED COMPENSATION PLAN

FOR NON-EMPLOYEE DIRECTORS

(2005 Restatement)

The “APOGEE ENTERPRISES, INC. DEFERRED COMPENSATION PLAN FOR NON-EMPLOYEE DIRECTORS” as adopted by APOGEE ENTERPRISES, INC., a Minnesota corporation, and first effective January 31, 1998, and as amended and restated in a document entitled “Apogee Enterprises, Inc. Deferred Compensation Plan for Non-Employee Directors (2005 Restatement)” effective January 1, 2005 is hereby amended in the following respects:

1. DEFINITIONS. Effective December 31, 2009 for elections made by the Participant for Plan Years beginning on or after January 1, 2010, Section 2.1.12 of the Plan Statement is deleted without a replacement (and all subsequent sections are renumbered).

2. ELECTION TO RECEIVE COMMON STOCK AT A LATER DATE IN LIEU OF CASH. Effective December 31, 2009 for elections made by the Participant for Plan Years beginning on or after January 1, 2010, the second sentence in Section 4.1 of the Plan Statement is amended to read in full as follows:

The amounts to be deferred will be in the form of a Common Stock credit to the Participating Director’s Deferred Stock Account, as set forth in Section 4.2 hereof, for the amount of the Retainer and Fees the Participating Director elects to defer.

3. CREDITS TO DEFERRED STOCK ACCOUNT. Effective December 31, 2009 for elections made by the Participant for Plan Years beginning on or after January 1, 2010, Section 4.2 of the Plan Statement is amended to read in full as follows:

4.2. Credits to Deferred Stock Account . Credits to each Participant’s Deferred Stock Account shall be made quarterly as of the last business day of each calendar quarter. The amount credited for each quarter shall include 25% of the amount of the annual Retainer for the applicable Plan Year for which the Participating Director chose to defer receipt of cash. The credit to the Deferred Stock Account shall be in the form of stock units in a number equal to the number of shares of Common Stock having a Fair Market Value, as defined in Section 4.5, equal to the amount of the Retainer and Fees so elected for deferral for the applicable quarter. Amounts credited to the Deferred Stock Accounts shall be rounded to the nearest one-hundredth share. In the event that a Participating Director elects to defer less than 100% of the Retainer and Fees in shares of Common Stock, he shall receive the balance of the payment in cash.

4. SAVINGS CLAUSE. Save and except as herein expressly amended, the Plan Statement shall continue in full force and effect.

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